Day 489: The Nose Knows

Genetic testing company 23andMe has found a genetic link to COVID anosmia—not as much of a coup as their blood type results but at least not the embarassment of their ice cream study (with the choices strawberry, chocolate, vanilla or you just don't like ice cream, do you?):

For these findings, the researchers again used data from more than one million people who consented to participate in 23andMe’s COVID-19 Study. By examining the differences in the genome between COVID-19 cases who did and did not experience loss of taste or smell, our scientists identified an association on chromosome 4 near the olfactory genes UGT2A1 and UGT2A2 (Figure 1 and Figure 2a).

The study is in preprint, and the genetic variant they found only makes one "about [sic] 11.5 percent more likely to lose their sense of smell or taste if infected". They also share some interesting data about anosmia by age: younger people are more likely to experience it, even controlling for general loss of smell among the elderly.

Massachusetts cases were up a fiftieth of a percentage point yesterday.

Day 483: At Half Vaxxed

With the recent approval of Pfizer's vaccine for 12-year-olds, Massachusetts has reached half-vaccinated status; that is, half the population is fully vaccinated already, including the waiting period. Tomorrow most of our restrictions will end.

Massachusetts cases were up a thirtieth of a percent yesterday. For comparison, COVID infections occur in only a hundredth of a percent of fully vaccinated people.

Day 475: Back to the Lab

The Commonwealth will be following the CDC's guidance to (mostly) return to normal on May 29th. The masking will continue on public transit and rideshares, and in hospitals, care facilities, and schools (of all places). Surprisingly, even Somerville, famed overreactionary city, is going along with the plan. (Yes, they announced it via Twitter.) Massachusetts cases were up a twelfth of a percentage point today.

With the craziness waning, theories are turning to where it all went wrong. Science writer Nicolas Wade wrote up the born-in-a-lab story on Medium this month, complaining that scientists are afraid to risk grants to investigate it and the press has ignored the theory.

“When I first saw the furin cleavage site in the viral sequence, with its arginine codons, I said to my wife it was the smoking gun for the origin of the virus,” said David Baltimore, an eminent virologist and former president of CalTech. “These features make a powerful challenge to the idea of a natural origin for SARS2,” he said.

Then Science published a letter of doubt about the origins of SARS-CoV-2.

We must take hypotheses about both natural and laboratory spillovers seriously until we have sufficient data. A proper investigation should be transparent, objective, data-driven, inclusive of broad expertise, subject to independent oversight, and responsibly managed to minimize the impact of conflicts of interest.

The New York Times put their finger in the wind and finally decided it was newsworthy, though they still take the side of a natural origin.

P.S. David Cole derides the purely human transmission angle, though with a sketchy argument that would also prove the discredited wet market origin theory.

Day 466: Age of Compliance

Although the FDA approved Pfizer's COVID vaccine for ages 12 and up yesterday, the kids are not quite complying yet. Jabbing has to wait for a recommendation from the CDC, which is meeting about it tomorrow.

Massachusetts cases were up a lucky thirteenth of a percentage point today.

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.