Day 459 Retrospective: Can't Quit the Crazy

May the fourth was day 459 of COVID in Massachusetts. The Star Wars holiday did not prevent reporting, and our cases were up a mere eighth of a percentage point yesterday, with deaths in the single digits. The Atlantic featured us once again, in their report on The Liberals Who Can’t Quit Lockdown. First, they noted that Brookline is still under the mask despite the lifting of the (always unnecessary) statewide outdoor mask mandate:

Leaders in Brookline, Massachusetts, decided this week to keep a local outdoor mask mandate in place, even though the CDC recently relaxed its guidance for outdoor mask use. And scolding is still a popular pastime. “At least in San Francisco, a lot of people are glaring at each other if they don’t wear masks outside,” Gandhi said, even though the risk of outdoor transmission is very low.

The angle of the article is political, so they profiled a wonk with local connections:

[F]or many, remaining guarded even as the country opens back up is an earnest expression of civic values. “I keep coming back to the same thing with the pandemic,” Alex Goldstein, a progressive PR consultant who was a senior adviser to Representative Ayanna Pressley’s 2018 campaign, told me. “Either you believe that you have a responsibility to take action to protect a person you don’t know or you believe you have no responsibility to anybody who isn’t in your immediate family.”

Goldstein and his wife decided early on in the pandemic that they were going to take restrictions extremely seriously and adopt the most cautious interpretation of when it was safe to do anything. He’s been shaving his own head since the summer (with “bad consequences,” he said). Although rugby teams have been back on the fields in Boston, where he lives, his team still won’t participate, for fear of spreading germs when players pile on top of one another in a scrum. He spends his mornings and evenings sifting through stories of people who have recently died from the coronavirus for Faces of COVID, a Twitter feed he started to memorialize deaths during the pandemic. “My fear is that we will not learn the lessons of the pandemic, because we will try to blow through the finish line as fast as we can and leave it in the rearview mirror,” he said.

And, of course, somehow it's always schools, Somerville, and our extra-crazy mayor:

Consider the experience of Somerville, Massachusetts, the kind of community where residents proudly display rainbow yard signs declaring in this house … we believe science is real. In the 2016 Democratic primary, 57 percent of voters there supported Bernie Sanders, and this year the Democratic Socialists of America have a shot at taking over the city council. As towns around Somerville began going back to in-person school in the fall, Mayor Joseph Curtatone and other Somerville leaders delayed a return to in-person learning. A group of moms—including scientists, pediatricians, and doctors treating COVID-19 patients—began to feel frustrated that Somerville schools weren’t welcoming back students. They considered themselves progressive and believed that they understood teachers’ worries about getting sick. But they saw the city’s proposed safety measures as nonsensical and unscientific—a sort of hygiene theater that prioritized the appearance of protection over getting kids back to their classrooms.

With Somerville kids still at home, contractors conducted in-depth assessments of the city’s school buildings, leading to proposals that included extensive HVAC-system overhauls and the installation of UV-sterilization units and even automatic toilet flushers—renovations with a proposed budget of $7.5 million. The mayor told me that supply-chain delays and protracted negotiations with the local teachers’ union slowed the reopening process. “No one wanted to get kids back to school more than me … It’s people needing to feel safe,” he said. “We want to make sure that we’re eliminating any risk of transmission from person to person in schools and carrying that risk over to the community.”

Months slipped by, and evidence mounted that schools could reopen safely. In Somerville, a local leader appeared to describe parents who wanted a faster return to in-person instruction as “fucking white parents” in a virtual public meeting; a community member accused the group of mothers advocating for schools to reopen of being motivated by white supremacy. “I spent four years fighting Trump because he was so anti-science,” Daniele Lantagne, a Somerville mom and engineering professor who works to promote equitable access to clean water and sanitation during disease outbreaks, told me. “I spent the last year fighting people who I normally would agree with … desperately trying to inject science into school reopening, and completely failed.”

In March, Erika Uyterhoeven, the democratic-socialist state representative for Somerville, compared the plight of teachers to that of Amazon workers and meatpackers, and described the return to in-person classes as part of a “push in a neoliberal society to ensure, over and above the well-being of educators, that our kids are getting a competitive education compared to other suburban schools.” (She later asked the socialist blog that ran her comments to remove that quote, because so many parents found her statements offensive.) In Somerville, “everyone wants to be actively anti-racist. Everyone believes Black lives matter. Everyone wants the Green New Deal,” Elizabeth Pinsky, a child psychiatrist at Massachusetts General Hospital, told me. “No one wants to talk about … how to actually get kindergartners onto the carpet of their teachers.” Most elementary and middle schoolers in Somerville finally started back in person this spring, with some of the proposed building renovations in place. Somerville hasn’t yet announced when high schoolers will go back full-time, and Curtatone wouldn’t guarantee that schools will be open for in-person instruction in the fall.

I think the argument for politics being at the root of crazy overreactions to COVID is backward, because the extreme risk aversion displayed in acts of COVID theater is an aspect of personality, not of politics per se. Politically motivated technocrats or liberals would be following the actual science instead. It's more likely that the other side has remained political, with its distrust of authority (and even paranoia), and oft-mocked concern for liberty.

Day 452: An End to the Crazy

Our governor has finally relented on the COVID-theater outdoor mask mandate, which comes to a well-deserved end this Friday, possibly due to the CDC's strange statement about the vaccinated not needing masks outdoors.

Massachusetts cases were up a seventh of a percentage point today.

P.S. The New York Times reported recently on how no one ever needed masks outdoors (except in the long-term face-to-face situations we've known about for a year now).

Day 450: Long COVID Fatigue

At Quillette, a brave and soon-to-be-cancelled writer compares "long COVID" to predecessors like chronic fatigue syndrome, and, surprisingly, transgenderism in "The Search to Explain Our Anxiety and Depression: Will ‘Long COVID’ Become the Next Gender Ideology?"

It’s important, as always, to emphasize that gender dysphoria has long been recognized as a real condition that afflicts a small portion of the population. What I’m describing here is an act of extrapolation, not of pure invention, whereby the existence of a legitimate diagnosis is co-opted by larger and larger portions of society. The same kind of trend has been going on in regard to homosexuality (which, to state the obvious, is also a very real phenomenon): To be gay (or bisexual) once had a fairly specific meaning in regard to one’s sexual tastes and behaviour. But teenagers now are encouraged to sort themselves into an ever-expanding typology of (often gauzily described) queer sub-variants—from allosexual (meaning non-asexual) to skoliosexual (“a sexual orientation that describes those who are sexually attracted to people with non-cisgender gender identities, such as people who are non-binary, genderqueer, or trans”). As in the latter case, these sexual identities sometimes mesh in complicated ways with gender identity—even though, as Angus Fox has described in his ongoing When Sons Become Daughters series for Quillette, many self-identified trans youth retreat to gender ideology precisely as a means of escaping (or at least delaying) the sexual changes and impulses associated with post-pubescent development.

One could even extend this pattern to the question of race. Every reasonable person will acknowledge that racism is a real phenomenon, and that the distinction between white and non-white can have concrete (and sometimes tragic) consequences for people who are victims of bigotry in Western societies. But out of this fact has sprung fanciful lexicons and hierarchies that purport to rank and encode fine racial distinctions, often (some might say, especially) in the case of privileged individuals who can’t explain how racism has affected their lives except by reference to abstract (and unfalsifiable) theories that cast the problem as an invisible, systemic malignancy generated by white people.

Another interesting point of comparison is the subclass of medical ailments known as “contested illnesses”—conditions such as chronic fatigue syndrome (CFS), multiple chemical sensitivities, and chronic Lyme disease, which don’t seem to exist except as a sort of crowdsourced belief system among individuals who claim to be afflicted. While none of these movements have attained anything close to the political and academic prominence of gender theory, their most politically engaged proponents echo the now-familiar idea that their problems can be traced to an outwardly undetectable condition whose denial generates its own separate form of suffering.

In the case of COVID-19, much attention has been focused on conspiracy theorists and lay quacks who claim the disease is a fraud. But there is also a pseudo-scientific movement that seeks to present its adherents as sufferers of a condition they call “Long COVID.”

As McMaster University psychiatrist Jeremy Devine recently wrote in The Wall Street Journal, some COVID-19 patients really do experience long-term effects that linger after the infection has left their body. But he adds that “such symptoms can also be psychologically generated or caused by a physical illness unrelated to the prior infection.” Moreover, he notes that a survey produced by Body Politic Covid-19 Support Group, a prominent driver of the Long COVID idea, indicates that “many of the survey respondents who attributed their symptoms to the aftermath of a COVID-19 infection likely never had the virus in the first place. Of those who self-identified as having persistent symptoms attributed to COVID and responded to the first survey, not even a quarter had tested positive for the virus. Nearly half (47.8%) never had testing and 27.5% tested negative for COVID-19. Body Politic publicized the results of a larger, second survey in December 2020. Of the 3,762 respondents, a mere 600, or 15.9%, had tested positive for the virus at any time.”

Echoing the idea of “self-identification” as the gold standard of gender identity, the Long COVID survey authors brushed aside these facts, arguing that “future research must consider the experience of all people with COVID-19 symptoms, regardless of testing status.” In this way, Long COVID also sounds a lot like chronic fatigue syndrome. In 2016, Devine himself, then a medical student, reported on a chronic-Lyme-disease group whose members, in many cases, “never had a Lyme infection in the first place. Those who explained away a negative Canadian test result often did so with a positive one from for-profit U.S. labs—so-called ‘Lyme specialty laboratories’—that offer testing with very high false positive rates.”

Massachusetts cases were up about a sixth of a percentage point today.

Day 448: The Most Compliant

The Boston Globe reports that Massachusetts has the lowest rate of "vaccine hesitancy" in the US at 7%. The only other state in the single digits (also 7%) was Vermont, while Wyoming is the most hesitant state.

Massachusetts cases were up a quarter of a percentage point today.

Day 441: Even the Queen

Female researchers at a couple of US universities have launched a formal study of COVID vaccines' unexpected effects on women's periods. (Women of childbearing age can participate in the research here.) Not surprisingly, platelets may be a factor:

There isn’t much research on how vaccination affects menstruation. But vaccines do stress the immune system, and the menstrual cycle sometimes responds to those types of changes. “The menstrual cycle is really dynamic, and it responds to tons of things,” Lee says.

There’s also a potential relationship between the nanoparticles used in the COVID-19 vaccines and changes in bleeding patterns. In some people, the nanoparticles end up creating a temporary immune reaction that kills off platelets, a type of blood cell involved in clotting, Clancy says. They regenerate quickly, but if someone has a bleeding event like a period just after they get a shot, it could make it heavier. She’ll be collaborating with Anirban Sen Gupta, a platelet researcher at Case Western Reserve University, to try to understand that potential mechanism.

Of course the real question is how such a pervasive side effect failed to come up in the initial trials considering that, apparently, women have been "regularly included in clinical trials [since] the 90's." Such glaring oversights don't exactly inspire confidence in the vaccines.

Massachusetts cases were up three-tenths of a percentage point yesterday, on what would have been tax day were we back to normal. Instead, the Commonwealth has followed the federal government in moving tax day to May 17th this year.

Day 438: No More Tears

The feds are recommending no more Johnson & Johnson vaccine after six cases of a rare clotting condition not unlike the one that sickened Vaxevria recipients in Europe. The suspension is temporary, but PlagueBlog hardly expects much uptake if they resume. Risk aversion seems to be at an all time high in the US.

Massachusetts cases are up a quarter of a percentage point today.

Day 436: Vaxzevria to Blame for VITT

Science reports on the causal connection between AstraZeneca's COVID-19 vaccine "Vaxzevria" and a rare clotting disorder scientists have dubbed vaccine-induced immune thrombotic thrombocytopenia (VITT). VITT has affected at least 222 European vaccine recipients and killed more than 30 of them (a rate of about one in a million).

While the disorder is similar to heparin-induced thrombocytopenia (HIT), the mechanism is only partly understood. The mRNA-based vaccines (Moderna's and Pfizer's) don't appear to prompt VITT, but suspicious clotting has already been reported for another viral vector vaccine, Johnson & Johnson's.

One in a million is a very small risk, possibly even smaller than the risk of a child under 10 dying of COVID, but several European countries have reacted by restricting the vaccine to the elderly. The article offers a glimmer of hope for Vaxzevria in lowering the doseage:

In AstraZeneca's phase III trial in the United Kingdom, a small number of people accidentally received a lower dose and had fewer side effects in general; perhaps the lower dose is less likely to trigger the kind of strong inflammation that boosts PF4 antibodies as well, the researchers say. And unexpectedly, those people were slightly better protected, perhaps because high levels of inflammation can actually block the formation of antibodies, Marschalek says. “Part of the problem might be that they just overdose” the vaccine, Greinacher says.

In local news, Massachusetts' cases have been holding around a third of a percentage point for the past week. (Today's numbers are not up yet.)

Day 432: The Brazilian Variant

The world is at 133 million total COVID-19 cases, with 31.5 million in the US, slightly over 13 million in Brazil, and slightly under 13 million in India. The rest of the top 10 countries have between 3 and 5 million cases each. China is currently #92, between Ghana, a nation of 31.6 million souls, and Kyrgyzstan, a nation of 6.6 million souls.

Massachusetts is at #15 among the states and is approaching 650,000 total cases. Despite ongoing hand-wringing over minor fluctuations in our case counts, the daily increase has remained well under half a percent since the holiday peak died down in early February. Yesterday, for example, was up only a quarter of a percent.

We do continue to lag in vaccination of young people (having only started the 55+ cohort this week) but our coverage in absolute doses is good, probably due to a combination of an older population and high uptake. We're also getting a bonus batch of vaccine this week. Barnstable County leads the Commonwealth in vaccinations, and it's a good thing because the P.1 variant on the Cape has given us the dubious title of the state with the most cases of the Brazilian variant.

P.S. More on P.1 from the Virological forum:

The detection of over 50 cases of the P.1 variant, a VoC that has been associated with increased transmissibility and reinfection, in less than a month in MA is concerning.

That many of these genomes appear to reflect multiple independent introductions of P.1 into New England, and transportation of this variant between several US states, points to likely widespread circulation of this VoC across the country. While our understanding of the increased transmissibility of the P.1 variant is still unfolding, the large cluster of identical and nearly identical genomes–a pattern of genetic diversity consistent with superspreading-- highlights the ongoing risk of rapid spread of SARS-CoV-2, and in particular for more transmissible lineages. The extent of community transmission of P.1 in Massachusetts and across the US is currently unknown, however, it is likely that the P.1 variant is already or will soon be circulating in communities and ongoing surveillance will be critical to understanding the trajectory and impact of the P.1 variant.

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

Day 399: The Vaccinated

In the sunset days of the pandemic, the world stands at 116.6 million cases, with almost 2.6 million deaths. The US is still in the lead with 29.5 million cases and half a million deaths. India remains at #2 with 11 million cases, and #3 Brazil is approaching that number. Both #4 Russia and #5 the UK have over 4 million cases, but Russia is increasing at double the UK's rate so should hold onto its ranking until #5 France catches up. At #6, Spain is increasing very slowly, while #7 Italy is on the rise with just shy of 3 million cases. China is currently at #85, just behind South Korea and about to be overtaken by Latvia, a country of under two million souls.

Rankings within the US have not changed much either, with Massachusetts still at #15. (Our cases were up a third of a percentage point today.)

The other day, US News reported 10% of American adults vaccinated. You can watch the numbers go up at the CDC vaccination tracker. Alaska and a few territories are currently over 30% half-vaccinated, while Connecticut, New Mexico, and the Dakotas are over 25%. The rest of New England is among the large swathes of the country with an adult population over 20% vaccinated.

Day 392: Where Has All the Flu Virus Gone?

Scott Adams got into a kerfluffle on Twitter that led me to an interesting article about the disappearing flu virus:

If the wearing of masks was capable of almost entirely removing influenza from circulation, as has been observed, then this approach would also eliminate SARS-CoV-2. Indeed, SARS-CoV-2 virions, which range from ~50 to 200 nm, are similar in size to those of influenza (~80 to 120 nm), adenoviruses (~90 to 100 nm), and other endemic betacoronaviruses, such as HCoV-OC43 and HCoV-HKU1 (~118 to 140 nm), which share the same genus as the novel virus. Since SARS-CoV-2, influenza, and various other respiratory viruses are largely spread by fine-particle aerosols in indoor settings, an intervention that works for one should logically work for the other. But in spite of the stringency of interventions, SARS-CoV-2 cases have skyrocketed. At the same time, infections of endemic betacoronaviruses, which should respond to NPIs in the same manner as SARS-CoV-2, have also largely disappeared [though adenoviruses have not].

Massachusetts cases were up a third of a percentage point both yesterday and today.

Day 390: Herd Immunity

David Friedman suggests that we've already hit herd immunity, not from the rapid rate of vaccination but from the flood of holiday cases:

I have been looking at the number of new cases per day, both for Santa Clara County and for the U.S., and the pattern is striking. Over the past month, number of new cases per day in the U.S. has gone down by a factor of about 2.4, for the county by a factor of about 3.5. Death rates are also down, although by much less, but one would expect death rates to lag case rates by a few weeks. I don't think the explanation can be the weather, since it's still winter. I don't think it can be vaccination because there has not yet been enough of it to substantially affect the case rate.

He's pretty optimistic that this is the end, all vaccination aside.

Johnson & Johnson's one-shot vaccine has emergency FDA approval.

Massachusetts cases were up a third of a percentage point today.

Day 384: Covered Up

Loyal readers may recall that the true extent of New York State's nursing home deaths came out back around Day 363. One might think that counting is hard, even if it's your job, but one would (allegedly) be wrong; the New York Post reports that Melissa DeRosa, Cuomo's secretary, admitted to covering up the numbers for fear of federal prosecution.

In addition to stonewalling lawmakers on the total number of nursing home residents killed by COVID-19, Cuomo’s administration refused requests from the news media — including The Post — and fought a Freedom of Information lawsuit filed by the Empire Center on Public Policy.

Instead, it only disclosed data on the numbers of residents who died in their nursing homes.

But after state Attorney General Letitia James last month released a damning report that estimated the deaths of nursing home residents in hospitals would boost the grim tally by more than 50 percent, Health Commissioner Howard Zucker finally released figures showing the combined total was 12,743 as of Jan. 19.

In other cover-up/miscounting news, Taiwan News reports on 150,000 missing pensioners in Wuhan:

On Wednesday, RFA [Radio Free Asia] published government figures released by the Hubei Civil Affairs Department showing that 150,000 names had vanished from the list of pension recipients over the first three months of 2020, when the outbreak in Wuhan was at its peak. These subsidies are paid to elderly residents in Hubei over the age of 80 who are in need of financial assistance.

[...]

Given China's rapidly aging population, an academic who wished to remain anonymous told RFA that there should be an increase in the number of elderly collecting such subsidies, much less such a dramatic decrease. The scholar believed that the massive burden on the health care system brought on by the outbreak could have indirectly "led to an increase in the number of deaths from other diseases."

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

Day 383: SSC and COVID Resurgent

Of 110 million coronavirus cases worldwide, 28 million have been in the US, with 500,000 deaths. India at #2 is nearing 11 million cases, and #3 Brazil is nearing 10 million (and also boasts its own strain these days). Russia and the UK are close as thieves with 4 million each, though some would say Russia's numbers are much higher, at least for deaths:

Russia’s official figures for the number of dead during the corona pandemic come from the Rospotrebnadzor authority and currently stand at 79,000 dead. However, on Monday the country’s statistics institute published data, revealing that the excess mortality in 2020 stood at 358,000, compared to the average deaths from the last couple of years.

Deputy Prime Minister Tatiana Golikova announced that 31 percent of the excess mortality rate in 2020 was due to covid-19, in other words 111,000 deaths. But the official death toll sent daily to the WHO is still below 80,000 dead.

Independent Russian newspaper Meduza now states that the Ministry of Health for the Moscow region has estimated that 98-100 percent of the excess mortality is due to the corona pandemic.

Loyal readers may recall that the New York Times killed Slate Star Codex back in the summer, for having gotten too much right about COVID. Since then, Scott Alexander has recovered from being set upon by the bullies of the legacy media, and has started up a new blog (Astral Codex Ten), where he has made new predictions of more coronavirus from more strains and also written up his thoughts on the weak tea science behind Vitamin D for COVID. His humor is back, too:

If blacks get coronavirus more often because of socioeconomic reasons, and also have lower Vitamin D, anybody looking at coronavirus infection rate without adjusting for race is suspect. Merzon and the Israelis didn't control for race (and Israel is quite racially diverse). Kaufman and the Quest team say they adjusted for race, but if you look at their paper, they didn't have access to race data for any participants, so instead they looked at what zip code they were in, coded it as majority-black or majority-white or whatever, and adjusted for that. I live in a majority black zip code, so apparently I'm black now. And my lived experience as a person of color, which I hear is more trustworthy than any scientific study, tells me this is a big enough loophole to invalidate the entire paper.

On the home front, Massachusetts is back up to #15 in the country, though yesterday's numbers were up only a fifth of a percentage point.

P.S. Massachusetts cases were up a quarter of a percentage point.

Day 374: Even the Yanomamo

The Guardian reports that ten Yanomamo children died of COVID last month. It's unclear what the definition of "children" is in this case (it may include 20-year-olds), but they also report seven previous Yanomamo victims under the age of two out of 32 total deaths. So it's clear that real children are involved this time, though it's not as clear that these deaths were from coronavirus rather than some other communicable disease with similar symptoms. PlagueBlog speculates that this unusually high death rate among children may be related to the lack of off-target vaccine protection in the isolated population.

In other international news, WebMD reports the failure of AstraZeneca's vaccine against South Africa's variant coronavirus strain B.1.351. The CDC tracks variant strains in the US, only one of which (B.1.1.7) has reached Massachusetts.

Massachusetts' cases were up a quarter of a percentage point today, due to the usual Monday reporting lull (of Sunday's data).

Day 373 Retrospective: Football Stadiums

Superbowl Sunday saw the first anniversary of Li Wenliang's death. Earlier in the week, the NFL promised all its stadiums for vaccination sites. Here in Massachusetts, the Patriots' stadium is already in use for vaccine administration. It seems to PlagueBlog that an open-air football stadium is hardly the most appropriate spot for medical treatment, but it seems that efficiency outweighs everything in these crazy time—unless you're talking about software.

Here in Massachusetts the feel-good news of the weekend was about an Arlington mom who built a more convenient vaccination scheduling website than the state's (which was already better than the feds') while on maternity leave. Also, cases were up three fifths of a percentage point on Sunday.

Day 372: But Sweden...

Last June, Nature published a much-cited paper modeling the efficacy of lockdowns vs. other non-medical interventions, "Estimating the effects of non-pharmaceutical interventions on COVID-19 in Europe" (where "intervention" means the government did it), and concluding that lockdowns, acting alone, saved three million lives. PlagueBlog will not be publishing the authors' names because the math is too embarassing, but Philippe Lemoine had no such compunctions when he tore the paper a new one back in a December blog post: "Lockdowns, science and voodoo magic".

Based on what I have seen by playing a bit more with simulations, it seems that the model tends to ascribe most of the reduction in R_t to whatever intervention took place after the peak of infections and was closest to that peak or, if no intervention took place after the peak, to the last intervention. This makes sense when you think about it. Indeed, if you assume that one intervention is responsible for the overwhelming majority of the reduction in R_t, the peak of the infections curve you infer is going to be located at the time this intervention took place. So both the infections curve and the deaths curve you infer are going to be shifted to the left or to the right depending on whether you assume that R_t collapsed sooner or later. Moreover, since both the infection curve and the distribution of the delay between infection and death are right-skewed, the death curve, on which the model is fit, is also going to be right-skewed. Now, when a curve is right-skewed, the fit is going to be worse if the peak of infections, hence also the peak of deaths, inferred by the model is to the left of the actual peak than if it’s to the right. So the model is better off ascribing most of the reduction in R_t to the intervention that happened closest to the peak of infections but after it, unless that intervention happened really too late after the peak.

It seems that it’s those purely mathematical considerations and the fact that lockdowns were implemented last and before or not too late after the peak of infections in every country, not the fact that lockdowns really are the only intervention that have a meaningful effect on transmission, which explain why the model reached that conclusion.

Well, not quite every country. Sweden never had a lockdown, so the model instead ascribes all non-medical efficacy to their last intervention, the cancellation of public events—a measure that had no effect elsewhere because it was followed by the supremely effective lockdowns, but was truly miraculous in Sweden. The paper doesn't show this explicitly because all European data has been pooled together, so Lemoine had to run his own unpooled calculations to see the Swedish miracle. Much of his post is devoted to the alleged malfeseance of the original authors in omitting this damning per-country calculation:

I actually think that not mentioning this fact about the country-specific effect in Sweden comes very close to scientific malpractice. It makes their main conclusion, which as [I] just noted can be seen to be implausible without any complicated modeling, very hard to maintain and I have a hard time believing they weren’t aware of that and that it’s not why they carefully avoided the topic in describing their results. In any case, what is clear is that, once you realize that the model was only able to find that no intervention except lockdowns had a meaningful effect on transmission by estimating a huge country-specific effect for Sweden, it becomes impossible to take that conclusion seriously.

The blog post was not the end of the story. A few weeks later, Nature finally published a Swedish response to the paper that it had been sitting on for six months and that largely agrees with Lemoine. (He discussed it and other responses in a second blog post.) It also inspired Lemoine to come up with his own theory about Swedish deaths, that the disease had progressed further there than elsewhere in Scandinavia. We at PlagueBlog still prefer the "dry tinder" theory of Sweden (that, rather than having an outsized number of deaths due to the lack of lockdowns, Sweden had more deaths because, after two mild flu seasons, they had an outsized population of fragile old people hanging on by the proverbial thread), but both may very well be true.

If you enjoyed that takedown, Lemoine also takes on the hydroxychlorquine question. In any event, PlagueBlog recommends that you check whether Sweden immediately disproves your theory before you publish it in a respectable scientific journal.

Day 368: Groundhog Year

So the groundhog saw its shadow, which means we'll be having six more months of COVID. PlagueBlog regretfully welcomes you to Year 2, Day 2 of COVID in Massachusetts.

In other annual news, the WHO has finally gone to Wuhan, more than a year after the outbreak began.

Despite the abysmal failure of the CDC's vaccine scheduling software, the new COVID year brings us more vaccinations than victims:

As of Monday afternoon, 26.5 million Americans had received one or both doses of the current vaccines, according to data compiled by the Bloomberg Vaccine Tracker. Since the first U.S. patient tested positive outside of Seattle a year ago, 26.3 million people in the country have tested positive for the disease, and 443,000 have died, according to data from Johns Hopkins University.

For reasons related to different software and general wariness, Massachusetts is behind in administering the vaccine:

The rollout in Massachusetts fell behind from the start. Other states, including Vermont, New Hampshire, Maine, and Connecticut began vaccinating nursing home residents and staff a week before Massachusetts started on Dec. 28. Since then, both of the required rounds of doses have been given at nursing homes in other New England states. In Massachusetts, which has one of the nation’s highest virus death rates in long-term care, most nursing homes have just completed their first round.

On the variant front, a travel ban against the South African variant strain continues to expand.

P.S. Massachusetts cases were up four ninths of a percentage point today.

Day 363 Retrospective: Undercounted

Time flies when you're COVID-fatigued! We're fast approaching Year 2 of COVID here in Massachusetts, but Thursday's banner story was out of New York State, where the New York Times reported some serious undercounting of nursing home deaths:

[...] Health Department officials made public new data that added more than 3,800 deaths to their tally, representing nursing home residents who had died in hospitals and had not previously been counted by the state as nursing home deaths.

The state’s acknowledgment increased the overall death toll related to those facilities by more than 40 percent. Ms. James’s report had suggested that the state’s previous tally could be off by as much as 50 percent.

The findings do not change the overall number of Covid-19 deaths in New York — more than 42,000, the most of any state — but the recalculation in the number of nursing home deaths illustrates how unprepared the nursing home industry was in the first and deadliest weeks of the pandemic.

Massachusetts' cases were up nine tenths of a percentage point on Thursday. (Note that MDPH case data has been in a much nicer format at Tableau since January 4th.)

Day 332: Boiling Frogs

The world is at 82 million cases, with the US nearing 20 million. Massachusetts remains at #18 among the states, with cases up one and a sixth percent today.

The vaccine frenzy is even more frenzied in the UK, where an anonymous doctor rails against it in "Boiling the bioethical frog", an article that links plenty of the science behind his own "vaccine hesitancy".

Also on the cure is worse than the disease front, AlJazeera reports on stillbirths caused not by the COVID pandemic itself, but by the reaction to it.

Day 326: Bowing Down to The Science

As Christmas fast approaches, the world is at 79 million cases. The US is approaching 19 million cases, with a third of a million deaths. COVID deaths are a contributing factor in our record-breaking annual death toll of over 3 million all-cause deaths. Massachusetts has risen to #18 among the states; our cases are up 1.5% today.

COVID variant B.1.1.7. continues to freak out UK and their neighbors, but its true scientific significance remains unclear.

Today Bruce Pardy complains in the Financial Post about that not-so-true science known as "The Science" before which we all must genuflect, whatever heretical beliefs we may maintain in private (or on blogs):

Scientific groupthink is now in vogue. Doctors who question the wisdom of pandemic lockdowns run the risk of being censored and cancelled. Thankfully, some are made of sterner stuff, such as Matt Strauss, a critical care physician and assistant professor of medicine at Queen’s University, and an early signatory of the Great Barrington Declaration. The declaration is a statement now endorsed by over 12,000 medical and public health scientists and over 38,000 medical practitioners expressing concerns about the science of prevailing COVID-19 policies. It asserts that lockdowns are producing devastating effects on short- and long-term public health that are disproportionate to the threat from the virus. As Strauss wrote in The Spectator in October, “mandatory government lockdowns amount to a medical recommendation of no proven benefit, of extraordinary potential harm, that do not take personal values and individual consent into account.”

Day 319: The End of Anti-vaxing?

Massachusetts cases were up 2% today and have exceeded 300,000; we are officially eyeing Alabama's #18 spot. While Florida has doubled down on allowing dining, California has gone freakishly far by banning outdoor dining, leading to outright rebellion and, of course, lawsuits. In a similar post-COVID spirit, Planet Fitnees calls a tool a tool in their loud protests of Boston shutting down gyms.

It's not clear whether the feverish "together-apart" celebration of the Pfizer vaccine will spell the end of anti-vaxing. The news cycle is a harsh mistress and has already jumped on an adverse reaction in Alaska. PlagueBlog can hardly imagine that the same innumerates who couldn't tolerate the 99.9% survival rate of COVID-19 will be able to put up with an equally miniscule rate of vaccine side-effects, but you never know.

Day 318: Alas, Phase 3

The world is at 73.6 million cases. The US at 17 million; #2 India is quickly approaching 10 million and #3 Brazil is slowly approaching 7 million. Late last week, Massachusetts edged out Colorado to return to #19 in state case totals. (Massachusetts cases were up one and a quarter of a percent yesterday and are up one and a third of a percent today.)

The Commonwealth of Massachusetts rolled back to Phase 3 Step 1 last week, and this week several cities and towns (Arlington, Boston, Brockton, Lynn, Newton, Somerville, and Winthrop) rolled all the way back to Phase 2 Step 2. Several more are expected to follow us over the cliff soon, while others have already declared their intention to keep the gyms and barstools open.

Day 315: The Pandemic Before the Pandemic

There's been a notable development in the collection of COVID-19 cases from 2018. Retrospective cases have been popping up for a while now, but the latest is special because it's a retrospective case of multisystem inflammatory syndrome in December. The patient was a four-year-old from the Milan area with no travel history, picked up (and a specimen preserved) by measles surveillance. More details on the case are available from the CDC letter.

Massachusetts cases were up 1.9% today.

Day 314 Retrospective in Numbers

The world had achieved 71 million total cases on December 11th, with 16 million of them in the US, along with 300,000 deaths. Massachusetts held steady at #20 in the US, with 280,000 cases, over 11,000 deaths, and a 2% increase in cases for the day.

The Biogen conference made the news again, with new genetic evidence that the event that never should have happened led to 333,000 cases in "at least 29 other U.S. states, Australia, Sweden and Slovakia."

Day 310: Unshared Streets

The world is at 67 million cases and 1.5 million deaths. The US is at 15 million cases, and California has taken back the #1 spot from Texas. Massachusetts has surged back to #20, with 11,000 deaths total; our cases are up 1.9% today.

Also in Massachusetts, in a particularly poorly-formatted web update, the people's republic city of Cambridge has announced they are unsharing their shared streets as of December 4th due to the onset of snow. Because of the general failures of communism sharing, they do not plan to reshare the streets under the same terms come spring.

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.

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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.

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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):

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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.

Day 274: White Halloween

The post-apocalyptic COVID landscape is the perfect setting for a white Halloween during which practically immune children are afraid to go trick-or-treating outdoors because of coronavirus. Also on Halloween in Massachusetts, the ever sketchy New England travel bubble was dealt another severe pinprick by the tit-for-tat addition of Connecticut to our quarantine list.

Massachusetts cases were up nine-tenths of a percentage point today.

Day 273 Retrospective: SNOVID-19

On Day 273, the US recorded 101,000 cases (by the Worldometers count), setting a local record, if not a world record. BNO also noted a weekly record of 500,000 cases. Despite some shuffling of the higher ranks (and plenty of panic), Massachusetts remained at #21 in US case counts. Cases were up about 1%.

"SNOVID" appears to have been coined by oldgrimalkin on Reddit, in honor of the unseasonable snowfall in Massachusetts on the day before Halloween. Also of coronaviral note on the 30th were a confirmed COVID case and a presumptive case in two captive Tennessee tigers. The victims, while seemingly recovered and unlikely to get within six feet of anyone, remain in quarantine.

Day 271: Reverse Marathon

India at 8 million cases is gaining on the USA's 9 million and change, while #5 France is planning a new lockdown for Friday. Most notable in the recent surpassers of #55 China is #54 Austria, a nation of only 9 million people none of whom are in the habit of eating bats.

Most notable among recent cancellations is the "postponement" of the second Boston Marathon to fall victim to COVID. It matters not that Massachusetts has fallen to #21 in case counts behind #20 Indiana despite our alleged COVID backsliding (otherwise known as "autumn"). Speaking of the weather, Chicago will "suspend" indoor dining starting on Friday, making for no dining out at all considering their climate.

The ever sketchy New England travel bubble has been dealt a severe pinprick by the addition of Massachusetts to Connecticut's quarantine list.

Day 268: Doubling Down

Thursday's cities and towns data (for Wednesday) reveals a slowdown of tourism COVID cases on Nantucket and the Cape. The red city rate (8 cases per 100k per day) remains below the state average (still 9 cases per 100k); this week's big outlier was Lawrence at 46 cases per 100k per day. (Middleton at 62 cases is just another small town outlier.) The data also includes county-level summaries for most real counties, plus the fake COVID county of Dukes and Nantucket.

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Day 264: More COVID Fatigue

On the COVID fatigue front, the Commonwealth seems to have tired of Wednesday as cities and towns day, and now will be releasing the data on Thursdays, allegedly by 4pm.

Day 262 Retrospective

Monday was notable for the COVID alert messages from the Commonwealth that were intended for residents of "red" cities, but went out to inappropriate people in wildly inappropriate numbers. Here at PlagueBlog headquarters, we got several alerts for both Everett and Chelsea, despite not being located in Everett or Chelsea, nor having set foot in Chelsea since before the plague began. PlagueBlog notes that spamming the wrong people is a good way to get your message ignored.

Day 257: In the Red

Since last we met, the US has exceeded 8 million cases, and several small-to-middling countries have passed the China point, including Portugal, a nation of ten million (only 1/144th its size). Despite the best efforts of Maryland and Indiana, Massachusetts remains at #20 among the states in case count.

Speaking of Massachusetts, there has been much hand-wringing today over the increasing "redness" of the state. It's not about politics but about cities and towns with average daily case rates of 8 or more (per 100,000) over the past two weeks. In fact at 9 cases per 100k the whole state is currently in the red, with outliers having case rates of up to 100, so the current rating system doesn't say much about a particular town's performance. Bigger, denser cities have more cases for the obvious reasons.

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Day 251: More Great Barrington

Brazil (at #3) has reached 5 million cases; #2 India is approaching 7 million, and at a pace that puts it in position to overtake the US eventually.

Governor Whitmer has been digging up Spanish Flu laws in an attempted end-run around last week's state supreme court decision striking down a 1945 law and her coronavirus restrictions along with it. PlagueBlog senses that this is not the right legal or temporal direction to be going in, and that the "burn your masks" lawyer will be back before their supreme court sooner rather than later.

AIER, after letting slip their involvement in the Great Barrington Declaration, has been reporting on the reaction to it, from scientists, the media, and the social media peanut gallery. Off-Guardian was not involved in the declaration, but assembles a lot of prior art of scientists and health care workers recommending against lockdowns.

Yesterday's weekly cities and towns data was the twenty-sixth such missive from the state. That's half a year, and the weekly reports only started in April. The coronavirus drama in Boston has actually been going on for 251 days since our first case, which is more than two-thirds of the year. Although the news just keeps on coming so does the COVID fatigue, so PlagueBlog will be reducing our publication schedule for the foreseeable future.

On to the data: while in recent weeks the Stop the Spread cities (with dotted borders) haven't been consistently ahead of other cities and large towns in case counts, this week you can see they're hotspots, along with Nantucket and the usual random smattering of small town outliers:

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Day 250: The Day the Movies Died

Wisconsin surged past Massachusetts yesterday, pushing us down to the #20 slot in case count. Though Maryland is at #21, Indiana is moving faster and may catch up soon.

Technically speaking, the movies will die tomorrow, when Regal closes all theaters in the US and UK. Parent company Cineworld is also closing all theaters, though this only affects the UK. They blame the lack of content coming out of studios, who have been holding back their big titles in hopes of better revenues post-pandemic. (PlagueBlog warns that there may never be a time after the pandemic.) Regal is the second-largest US movie theater chain. The largest chain, AMC, has kissed and made up with Universal Studios and plans to remain open.

The New York Post reprinted the Great Barrington declaration last night, and it's now surpassed 100,000 signatures.

On the irony watch, Father John Jenkins, President of Notre Dame and target of his own home-grown Stasi after he failed to wear a mask to the Rose Garden super-spreading ceremony, has added injury to insult by testing positive for COVID. A faculty no-confidence vote against him has been postponed for the moment, and students are circulating petitions for his removal.

Massachusetts' case numbers are delayed today, as is the weekly towns and cities data. In other local news, the mayor of Boston announced a delay in the phased reopening of Boston's public schools for off-line education, over a minor increase in the positivity rate here. Some have attributed our rising positivity to a drop in testing the well for COVID, rather than to any meaningful change in the local coronavirus situation.

P.S. Massachusetts' cases were up two-fifth of a percentage point today.

Day 249: Neo-Neo-Neovisicide

The reprieve for Danish mink has been called off, and now they're getting even more culled than the unfortunate Dutch mink. Besides recovered mink at infected farms, they're also culling every mink on farms within 5 miles of any infected farm, because somehow they pose a threat to humans. PlagueBlog hopes they don't kill all the human patients in hospitals within five miles of an infected hospital.

In England, the recent underreporting of 16,000 COVID cases has been traced to...Microsoft Excel:

Public Health England (PHE) collected data from commercial firms that analysed the swab results to see who tested positive or not, and receved the information in files with the values separated by commas.

Using comma separated values (CSV) in files is common practice for handling data.

PHE loaded the files into Microsoft Excel spreadsheet templates to be entered into a central system used for government contact tracing and reporting dashboards.

However, the PHE developers used the original binary .XLS file format for Excel which first appeared in 1987.

[...]

BBC reported that thanks to the old file format being used, each Excel template was limited to recording around 1400 cases.

Any further cases than that were ignored by template, and led to 15,841 going unreported between September 25 and October 2 which may have led to people being unaware of COVID-19 exposure in that time.

Massachusetts' cases are up about a third of a percentage point today. In other local news, Falmouth High School went virtual yesterday after an unknown number of virtually immune students "attended a party this weekend in Woods Hole while not wearing masks and not practicing physical distancing." As usual there was much hand-wringing from the puritan administrators of the school.

Day 248: The Great Barrington Declaration

Today Japan, a nearby island nation with less than a tenth of the population of China, has exceeded China in cases, taking on the #45 spot.

The Great Barrington Declaration is only surprising in that the authors had to travel in secret to Great Barrington, MA (a little town in the Berkshires featuring a weird castle, Bard College, and a perfectly average 14-day case rate) to formulate it. The declaration's "Focused Protection" amounts hiding grandma while acquiring herd immunity through normal living for healthy, low-risk young people and school children. They were also interviewed briefly on LockdownTV. The general public as well as other scientists and health care workers are encouraged to sign the declaration.

The Michigan Supreme Court struck down the Emergency Powers of Governor Act (the target of the petition from a week and a half ago) on Friday, though it's still unclear to the Governor whether and for how long her now-illegal orders stand. The attorney behind the case says to "burn your masks".

Massachusetts' cases are up almost two-fifths of a percentage point today.

Day 247: Stasi Fail

India made the BNO News with 100,000 COVID deaths, though by Worldometer's standards they've been there for a few days now. Nepal, a nation of fewer than 30 million souls (that is, 1.4 billion fewer than China), bordering China (due to the latter's occupation of Tibet), now, somehow, has reached the #44 spot, with more cases than #45 China.

On the because it worked so well for Germany front, the University of Notre Dame's Stasi-style snitch-on-a-classmate website has been repurposed by enterprising students to snitch on the university president for not wearing a mask to the Rose Garden super-spreader event. (It seems the "super" spreading may have happened at the debate prep, instead, where the now-infected Trump, Bill Stepien, Kellyanne Conway, Hope Hicks, and Chris Christie were present.)

Business Insider is optimistic about President Trump's condition, so here's a little humor about it from "Whiskey Fueled Tirade" at DuffelBlog: Walter Reed medics tell President to return during sick call hours:

Medics and corpsmen at the Walter Reed National Military Medical Center responded with the poise and compassion characteristic of their profession when the president arrived at the military’s flagship hospital earlier last evening.

“I told him the same thing I tell everybody when they show up all sad-faced and mopey while we’re closing the clinic,” Spc. Will Farmer, a medic assigned to the hospital, said as he smoked a cigarette near the executive sick call entrance. “Take some Motrin, drink water, and come back at 0430 when sick call starts hours if you really think you need to be seen. I see it all the time. Last week some supreme court lady was trying to get an appointment after sick call hours.”

“He’s probably just trying to get out work, or a debate or something.”

In science news, ProMED reports on several papers suggesting Parkinson's Disease may be one of those allegedly unusual long-term COVID-19 sequelae. Although parkinsonism is better known as as a consequence of other viral infections like the flu, and so far there seems to be only the one case report from Israel, it is something to watch out for.

Massachusetts' cases were up about half a percentage point again today. In other local news, Patriots quarterback Cam Newton has tested positive. Today's game has been postponed until Monday after an opposing team member also tested positive. Also, Worcester has cancelled Halloween, apparently in accordance with CDC guidelines suggesting that virtually-immune children do boring stuff at a distance to avoid COVID instead of trick-or-treating.

Day 246: Even the Rose Garden

The world is at 35 million coronavirus cases, with #3 Brazil nearing 5 million. Japan (#45) is asymptotically approaching the China mark, while #46 Nepal and #47 Czechia chug along behind them. In the US, Missouri has taken the #18 spot from Massachusetts, and #20 Wisconsin is only a couple of days away from beating us as well.

The New York Times reports on the growing cluster of cases tentatively attributed to the Rose Garden ceremony for Amy Coney Barrett (or, more likely, the indoor reception that followed).

P.S. Massachusetts' cases were up half a percentage point today.

Day 245: Even the God Emperor

President Trump tweeted (of course) that he and the First Lady tested positive for COVID-19, following news that an aide, Hope Hicks, was infected. The meme-imperial couple are "well", which PlagueBlog takes to mean asymptomatic. Their quarantine schedule may affect the second debate. The Vice President and Second Lady have tested negative.

P.S. Massachusetts' cases are up four-sevenths of a percentage point again today. (That's 761 cases, keeping us just barely ahead of Missouri for another day.)

P.P.S. NBC has updates on the President's "low-grade fever" and trip to Walter Reed, as well as Melania's "mild cough and headache."

Day 244: Even the Neanderthals

An article in Nature claims that The major genetic risk factor for severe COVID-19 is inherited from Neanderthals. But not all post-Neanderthals have it; the particularly problematic genes seem to be more common in South Asians than in any other out-of-Africa group. (Africans rarely carry Neanderthal genes.)

MedPage Today reports that ECMO (extracorporeal membrane oxygenation) wasn't as universal a failure for COVID patients as previously suspected. (It made ventilators look helpful.) It turns out that only about 40% of patients died in hospital afterwards. However, the follow-up on the allegedly surviving 60% wasn't really solid or long-term enough to be entirely convincing.

Forbes reports that Mississippi's mask mandate expired peacefully in its sleep last night.

Massachusetts' cases are up four-sevenths of a percentage point today. While the general grouping of our "red" cities (Lawrence, Framingham, Revere, New Bedford, and the Islands) hasn't changed much, things are getting a little more infected. (Also, maps from last week have been corrected due to PlagueBlogger error.)

(Pop out.)

Day 243: No One Here Cares

As the world hits 34 million cases, local puritans continue to be surprised at college students' disregard for a disease that poses little threat to them personally. In this case the culprits were unmasked Boston College football players failing to be somber and socially distant in a "tightly packed locker room" after beating Texas State 24–21 in a comeback victory. Since dirty football players are expected to go to locker rooms after games and no grandmas are known to have been killed by COVID-negative athletes, it's not clear what their offense was or what exactly they weren't caring enough about.

In other young immortal news, a 48-year-old senior non-comm in the Army Reserve died of coronavirus, making him only the eighth US service member COVID death. The military’s COVID death rate is around 0.015%, with only one active duty serviceman having died (the sailor from Germ Boat #23).

NPR has been reporting on life in the fake school trenches. You'd think we'd have a hard number, but NPR could only provide an estimate that about 50% of school districts went virtual this fall. NPR is ominous about parents "reaching a breaking point", with moms leaving the remote workforce after failing to both work and parent full-time at home, leaving their kids at home alone with a computer while they go out to work, or paying for daycare to supervise their children's fake school day. The latter is most notable for recreating all the risks of school for the children and their stand-in teachers, at extraordinary expense to their parents. As if all of that weren't bad enough, a second NPR article reports on the compound consequences of parental unemployment and childhood social isolation.

In cute and furry news, a New York company, Applied DNA Sciences, has responded to the crowded COVID vaccine market by creating a vaccine for cats. It's already in clinical trials "upstate". PlagueBlog admires their ingenuity, and also hopes that this doesn't turn into another Lyme disease situation where a vaccine is available for pets but not for humans.

P.S. Massachusetts' cases were up two-fifths of a percentage point again today. The cities and towns data is out and shows some activity on Nantucket and in the north around Lawrence. (Maps tomorrow.)

Day 242: Not Taking COVID Seriously

Despite the recent lockdown, Israel is reported to have the highest weekly infection rate in the world and a daily death rate higher than the US. Though this wasn't their first lockdown, their plan seems to be to continue with socialism lockdowns until it finally works.

Massachusetts cases were up two-fifths of a percentage point today. Missouri (#19) is on the rise and may pass #18 Massachusetts in another day or two. Another steady climber at more than 2,000 cases a day is #21 Wisconsin.

In local news, BU is working itself up to suspend 20 underage students for attending an outdoor "beer party", not because underage drinking is illegal (it is) or because they were anywhere near the limit on outdoor gatherings in Boston (they weren't), but because they "won’t take COVID-19 seriously." (PlagueBlog would not be here blogging today if, back in the day, we'd gotten tossed out of institutions of higher education for taking beer more seriously than AIDS.)

Day 241: One Million Deaths

The news has settled on today as the day to declare a million coronavirus deaths worldwide. COVID-19 now rivals the largely forgotten Hong Kong flu in fatality, and has only 99 million deaths to go to equal the Spanish flu. (Some put the death toll of the Spanish flu at only 50 million, but 'tis the season to put the worst possible spin on everything.)

Florida let 'er rip on Friday and people are still complaining about the bars being packed there since reopening. Dr. Fauci is very concerned.

Massachusetts' cases are up a third of a percentage point today.

Day 240: Madrid Rebels

BNO News has declared a million coronavirus deaths worldwide, while (at the time of writing) Worldometers remains a few hundred deaths short of that milestone. But #2 India has reached six million cases.

Spain (at #7) is having a flare-up in Madrid, with more than double the country-wide average cases per fortnight (and more than seven times the average in the UK). The national health minister called for Madrid to lock down, but the regional government has refused to do so, apparently out of economic concerns. While much of the increase can be attributed to better testing and the death rate is down, ICU capacity in Madrid remains a concern.

In local news, Nantucket's COVID wave continues. Tourists are part of the problem, though some of the new cases are among locals and haven't been traced yet.

P.S. Massachusetts' cases are up four ninths of a percentage point again today.

Day 239: More Vitamin D

The world has reached 33 million coronavirus cases, and is very close to one million deaths (prompting the WHO to prognosticate the next million deaths). India is about to reach 6 million cases, though their death rate is minuscule with not even 95,000 deaths so far. Now #43, Poland has crossed the China line.

The well-known benefits of Vitamin D continue to appear in studies, including this PLOS ONE article that concluded:

The association between lower SARS-CoV-2 positivity rates and higher circulating 25(OH)D levels remained significant in a multivariable logistic model adjusting for all included demographic factors (adjusted odds ratio 0.984 per ng/mL increment, 95% C.I. 0.983–0.986; p<0.001). SARS-CoV-2 positivity is strongly and inversely associated with circulating 25(OH)D levels, a relationship that persists across latitudes, races/ethnicities, both sexes, and age ranges. Our findings provide impetus to explore the role of vitamin D supplementation in reducing the risk for SARS-CoV-2 infection and COVID-19 disease.

Unfortunately, impetus is far from proof of the efficacy of vitamin D supplementation, though this study did go pretty far in separating out vitamin D levels from other confounding factors.

Fortunately, a previous study (dated next month but previously PlagueBlogged) already showed the efficacy of administration of vitamin D in treating hospitalized COVID-19 patients.

Massachusetts' cases are up four ninths of a percentage point today.

Day 238: Wantonly or Recklessly

On the international COVID scene, the news puts Spain at 700,000 cases after a week of about 10,000 cases a day (fueled by improved testing). Worldometers already has them at 735,000 cases (and at #7); #11 France is also experiencing record case counts, bringing them close to 500,000 cases total. Hospitalization and death rates there are also three to four times higher now than in August. Lower down on the list, #44 Poland is rapidly approaching the China mark.

In domestic news, Virginia Governor Dr. Ralph Northam and his wife have tested positive for coronavirus. He claims to be asymptomatic; they may have caught it from the hired help at the Executive Mansion.

In Michigan, 500,000 residents are petitioning to revoke the open-ended Emergency Powers of Governor Act, one of two Michigan laws permitting the Governor to declare a state of emergency. If they succeed (either by the legislature voting in favor of it or, failing that, by ballot initiative), the remaining law will require that a state of emergency be renewed by the legislature on a monthly basis. It seems the Republican legislature is expected to approve the petition, but it may take up to 100 days for the government to certify at least 340,047 of the signatures.

The New York Times reports the Massachusetts grand jury indictment of superintendent Bennett Walsh and medical director Dr. David Clinton, formerly of the Holyoke Soldiers' Home.

Each man was indicted on five counts for two charges; the specific charges were for caretakers who “wantonly or recklessly” permit or cause bodily injury and abuse, neglect or mistreatment of an older or disabled person.

P.S. Massachusetts' cases were up three sevenths of a percentage point again today.