Day 170: In a cavern, in a canyon, excavating for a mine...

Deaths worldwide have topped 600,000. In the US, Florida is now well in the lead of Texas and is eyeing California's #2 spot. Massachusetts cases are up a quarter of a percentage point today.

The mainstream news of the day seems to be the New York Times' sketchy take on a study out of South Korea, in which the Korean scientists were careful to state that they did not determine the direction of transmission, or even that transmission was familial at all. Nevertheless, the Times jumps to the conclusion that children aged 10 and up can transmit the disease as well as adults. Just one of those coronavirus "facts" you'll probably need to conveniently forget later...

The interesting news of the day, however, is a commentary in Independent Science News on the lab origin theory of the current pandemic. PlagueBlog readers may recall previous made-in-a-lab theories involving the mysterious coronavirus sequence known as RaTG13, and Dr. Shi of the suspiciously-located Wuhan Institute of Virology. This theory differs on a few points. It accepts RaTG13 as a genuine, natural coronavirus, spends a good deal of time debunking the opposition (an oft-cited review in Nature from March), and tells a new story about COVID-"19" in which it is actually COVID-12:

The story begins in April 2012 when six workers in that same Mojiang mine fell ill from a mystery illness while removing bat faeces. Three of the six subsequently died.

In a March 2020 interview with Scientific American Zeng-li Shi dismissed the significance of these deaths, claiming the miners died of fungal infections. Indeed, no miners or deaths are mentioned in the paper published by the Shi lab documenting the collection of RaTG13 (Ge et al., 2016).

But Shi’s assessment does not tally with any other contemporaneous accounts of the miners and their illness (Rahalkar and Bahulikar, 2020). [...]

Fortunately, a detailed account of the miner’s diagnoses and treatments exists. It is found in a Master’s thesis written in Chinese in May 2013. Its suggestive English title is “The Analysis of 6 Patients with Severe Pneumonia Caused by Unknown viruses“.

The authors had the thesis translated, from which it became clear the miners suffered from a disease very similar to COVID-19, and not from fungal infection. In fact their doctors consulted with China's expert on SARS and sent samples to the Wuhan Institute of Virology, from which (they hypothesize) the virus later escaped.

The flurry of virus-hunting behavior in the mine by Dr. Shi and others after the miners fell ill is thus deeply suspicious, as is their publication of RaTG13 and a prior subsequence without any comment on the miners or their disease, instead asserting that the distant Yunnan province mine where they collected their samples was "abandoned".

To account for the differences between RaTG13 and its closest coronaviral relative, SARS-CoV-2, the authors propose viral evolution within the six miners as their "Mojiang Miners Passage (MMP) hypothesis". Specifically, the virus evolved in their lungs, an unusual locus of coronavirus infection (at the time) that they believe was particularly conducive to the recombination of RaTG13 and other coronaviruses from the mine into SARS-CoV-2.

They also posit an explanation for the long delay between COVID-12 and COVID-19:

Our supposition as to why there was a time lag between sample collection (in 2012/2013) and the COVID-19 outbreak is that the researchers were awaiting BSL-4 lab construction and certification, which was underway in 2013 but delayed until 2018.

We propose that, when frozen samples derived from the miners were eventually opened in the Wuhan lab they were already highly adapted to humans to an extent possibly not anticipated by the researchers. One small mistake or mechanical breakdown could have led directly to the first human infection in late 2019.

In conclusion, they call for an independent investigation of the Wuhan Institute of Virology, as well as of the "conflicts of interest" they see as suppressing the escaped-from-a-lab hypothesis.

PlagueBlog notes there is something off about the notion that six miners breathing bat guano could substitute for the missing human evolution phase of SARS-CoV-2 that has made it so stable since. It is particularly mysterious how all six of them fell so ill at the same time, and yet the mine has failed to start the number of pandemics this rate of attack would seem to promise. Bats are not known for flying about in tiny masks, so perhaps the mine workers themselves did something unusually unsanitary. They were allegedly cleaning out bat guano at the time they fell ill, which doesn't seem like the most productive or typical miner employment.

PlagueBlog recommends that, when you see a bat, you run screaming in the other direction. (A mask should not be worn for this purpose, as it impedes proper screaming.) In particular, do not gather or eat its guano for any reason whatsoever.

Day 169: The Massachusetts Miracle

Massachusetts has gone from below-average unemployment for the country to the #1 spot, clocking in at 17.6% unemployment for June. The Boston Globe blames it on our coronavirus response. Also not very encouragingly, our case count is up a third of a percentage point today.

A new preprint from the Netherlands concludes that aerosol transmission is "inefficient" compared to droplets, especially in those with few to no symptoms. They studied only a handful of (healthy) subjects with lasers to determine what sorts of spray volumes they coughed up. In line with previous research, they found not much variation between people in their spray production regardless of size, age, or sex, but they did have one super-moist subject (17 times more volume than average) whom they postulated might be a super-spreader, were they infected.

For coughing, the volumetric distribution measured using laser diffraction shows that on average 98 ± 1% of the volume of the spray is contained in the large drops (100-1000 μm).

The paper becomes less satisfying when the authors fall back on the physics and some experiments with artificial aerosols to determine what happens to the remaining ~2% of spray, but there are some entertaining graphs to compensate for the high level of speculation.

The American Constitution Society takes a whack at the question of whether face masks are constitutional, and answers yes.

Day 168: Even the Deer

The world has reached 14 million cases. The US is at 3.7 million cases, while #2 Brazil has hit 2 million cases and #3 India has achieved 1 million. Spain continues in their miraculous defeat of death through bureaucratic incompetence. Massachusetts cases are up a quarter of a percentage point, not to gloat or anything.

Deer have not actually been shown to get coronavirus, but you wouldn't know it from driving around Georgia, where the News & Observer reports that some card has been postering the roadkill with COVID-19 messaging:

A few folks are duly concerned about the specificity of COVID-19 PCR-based tests (having already given up the ghost on the wildly inaccurate serology tests). A June paper in the New England Journal of Medicine estimated their specificity at 70%, based on Chinese clinical studies rather than optimistic theoretical estimates from the test manufacturers themselves. That adds up to a whole lot of false negatives.

The situation of a hospitalized patient with obvious COVID testing negative has been pretty well understood all along, but it's worth looking into the consequences of wide-scale testing with a test that doesn't necessarily pick up a useful number of COVID cases. The paper goes into some numbers on this:

If the test sensitivity were 95% (95% of infected people test positive), the post-test probability of infection with a negative test would be 1%, which might be low enough to consider someone uninfected and may provide them assurance in visiting high-risk relatives. The post-test probability would remain below 5% even if the pretest probability were as high as 50%, a more reasonable estimate for someone with recent exposure and early symptoms in a “hot spot” area.

But sensitivity for many available tests appears to be substantially lower: the studies cited above suggest that 70% is probably a reasonable estimate. At this sensitivity level, with a pretest probability of 50%, the post-test probability with a negative test would be 23% — far too high to safely assume someone is uninfected.

The paper's conclusions aren't particularly notable, and Neil Kurtzman tries to expand on them for the Mises Institute, unfortunately unsuccessfully, because he just pulls a number for specificity (false positives) out of his gluteus and runs with that. PCR tests are, in fact, close to perfect when it comes to not mistaking bits of other things for your target virus, and there are, in fact, no false positives to speak of (unless you're speaking of antibody tests, and we do not speak of those).

It's no good to work through the Bayesean math starting from a gluteal value for specificity. The real reason there are no false positives coming out of Asturias, Spain (the mystery that Kurtzman found so hard to swallow) is that Spain doesn't report serology results anymore. All testing aside, one should not be surprised at zeroes coming out of Spain, where they can't even manage to count their own dead like we do in every other first-world country.

On the lockdown skepticism front, Sweden has returned to their background death rate. Argentina's severe lockdown has not produced the positive results one might have expected, if one thought locking down was any kind of useful medical response, leading to some dissent among the medical ranks:

¿Por qué se instrumentó una cuarentena para individuos sanos cuando no hay registro de tal restricción en la historia de la humanidad? ¿Qué criterios científicos y particularmente epidemiológicos se aplicaron para extender la cuarentena total a cinco provincias sin casos y a otras seis con uno o dos casos? ¿Por qué no se le dio suficiente importancia a la producción natural de anticuerpos por vía del contagio en población no vulnerable, privilegiando la inmunidad adquirida mediante vacunas?

If you enjoy rhetorical questions in Spanish as much as our PlagueBlog staffers do, there are a total of sixteen of them at the link above. El Presidente does not appear to have answered any of them yet.

Day 167: Neo-Neovisicide

ProMED reports that a twenty-fourth mink farm in the Netherlands has been found infected (despite strict isolation protocols) and "will be cleared as soon as possible." About 20% of mink farms in the Netherlands have been infected and culled at this point, a number suspiciously close to the (human) level of infection one might expect from their government's original (human) herd immunity plans.

In Denmark, a second and third farm have been found infected. Over half of the herd of 5,000 mink at the third farm were positive, and all were slaughtered at the beginning of July. In addition, the family dog at the first Danish farm has tested positive, but apparently escaped the wholesale slaughter.

Massachusetts cases are up a fifth of a percentage point today. The MDPH cities and towns report was even more mauled than we at PlagueBlog Headquarters initially thought; they are no longer reporting test counts per person, but are now giving an actual total of all tests (so Boston jumped from 97,288 persons tested to 141,184 tests performed). They are also not reporting case rates any longer. (Some rate maps survive in the report, but the data is gone.) While case rates can be calculated from the case totals and public population information, the MDPH doesn't report the actual "denominators estimated by the University of Massachusetts Donahue Institute using a modified Hamilton-Perry model" that they used, so a direct comparison with the rates they used to report would require some gymnastics not really merited by our current low numbers.

They are still reporting positivity (if you care for that sort of thing) as well as more "last 14 days" data (that was easily derived from the previous, fuller reports), and one useful thing having to do with percent positivity: whether it's going up or down. So here is our current take on the last 14 days:

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Day 166: Masked Lives Matter

While the US remains comfortably in the lead with our 3.6 million cases, Brazil is nearing 2 million cases and India is approaching 1 million. Iraq has passed the China point; up next: Indonesia. In the US, Florida has topped 300,000 cases with Texas trailing only a few thousand cases behind.

Massachusetts is up a fifth of a percentage point again today. The MDPH has restructured the weekly cities and towns report yet again, so maps will have to wait until the PlagueBlog punch-cards have been re-punched to match.

While you're waiting, consider the sudden flurry of mask requirements—not from state governments with health departments devoted to population-level health issues, not even from marauding mayors with health departments in their heads devoted to randomly contradicting the real health departments' decisions, but from overpriced coffee shop chains and purveyors of cheap Chinese crap products.

It started reasonably enough with the airlines, who are flying passengers from jurisdiction to jurisdiction without a lot of federal guidance. But then Costco got involved, as if this were some Twitter fad that they had to have an opinion on, and not a local regulatory matter like what hours they get to sell beer (if at all).

Before you could say masked lives matter, Starbucks joined the fray, requiring masks at "company-owned locations"—as if a customer can tell a company-owned Starbucks from an independent vendor of their distinctively nonsensical range of drink sizes. Next, in their first bid ever to help mom-and-pop businesses, Walmart announced they will be requiring masks next week, as will supermarket chain Kroger's.

On the anti-mask front, Georgia Governor Kemp has struck down the mask regulations he already warned local jurisdictions not to make. PlagueBlog encourages him to lock down all Starbucks, Costcos, Walmarts and Krogers, because no man can serve two health departments—never mind serving every CEO who thinks he's the Surgeon General now.

Day 165: Even the Cans

Fox News reports on an aluminum can shortage caused by less soda drinking from fountains and more at home, making some soda varieties scarce. This may not seem like the most important coronavirus news of the day, but PlagueBlog feels that it beats overwrought stories about "record high" death tolls in states where they can still easily enumerate the dead in a brief news article. Let us know when you have 21 pages of obituaries down there.

PlagueBlog readers may recall the theory that previous infection by other coronaviruses has provided some stealth immunity to SARS-CoV-2. A group of Italian researchers turned this theory on its head with their June commentary in BMJ Global Health, in which they theorized that previous infection by other coronaviruses (or by SARS-CoV-2 itself) actually makes COVID-19 worse. Mild cases occur in the immunologically naive, while severe cases, they postulate, are caused by antibody-dependent enhancement (ADE), a phenomenon in which viral infection and reproduction are aided by binding to antibodies. ADE is known from HIV and other coronaviruses, and has already been mentioned as a potential roadblock to COVID-19 vaccine development.

As if that wasn't bad enough, Reuters reports on some depressing projections from British scientists of up to 120,000 deaths from COVID-19 next winter. That's in addition to their record 45,000 so far, which was already the third-highest death toll in the world and the second-highest death rate per capita among non-city-states (after Belgium).

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

Day 164: Faxing Like It's 1989

The world has reached 13 million coronavirus cases. Although the international rankings haven't changed much, the news noticed that #8 Mexico hit 35,000 deaths, moving it ahead of Italy into 4th place behind the UK in deaths. In the US, it looks like Florida has solidified its lead over Texas and is now on its way to catching up with California.

The New York Times reports on Texas' and other states' struggles to deal with faxed COVID-19 test results from multiple small labs that aren't entirely set up for the 21st century. In Houston, the ICUs are half-full of COVID-19 patients, with the proportion still rising, and an excess of Hispanic and Black patients compared to the local population. (The article does not mention what has become of the usual ICU patient population that would be in those beds.) Under a misleading headline, the New York Times actually reports on the excess of pregnant Hispanic and Black women exposed to coronavirus and what this may say about the true coronavirus statistics by race.

Poynter documents the apparently permanent loss of local newspaper staffs to coronavirus closures. Also on the journalism front, Ars Technica of all places tears the New York Times a new one over their reporting of a non-existent change in the WHO's stance on airborne transmission last week:

In its updated scientific brief on transmission, the WHO said basically the same thing it has said for months on airborne transmission. That is: the question of whether SARS-CoV-2 lingers in the air is a topic of active discussion, and, while it may be possible in some settings, the data in aerosol transmission so far is inconclusive or unconvincing. But, as always, the WHO welcomes more high-quality research on this topic.

Quillette reported a while back about misreporting of the WHO's stand on masks, and more generally on the poor outcomes to be had by telling people to wear masks "in public" rather than in specific high-risk situations.

P.S. Massachusetts cases are up a fifth of a percentage point today.

Day 163: Don't Be the Pigeon

Florida has responded to Texas' lead with a record day of 15,000 cases, but PlagueBlog believes Texas can catch up, at least temporarily. Here in Massachusetts, cases are up a fifth of a percentage point.

An essay on Medium, "Superstition in the Pigeon": Can Lockdowns Really Stop Death? has an unusually clear analysis of the shift from the reasonable and limited goal of flattening the curve for the sake of hospital capacity to our current superstitious health-theater effort at full-on coronavirus suppression.

The high point of Stacey Rudin's analysis for most people may be the story of a 1969 Antarctic expedition that had been effectively quarantined for 17 weeks when one of the researchers came down with a cold and spread it to seven others.

With outcomes like this, one would assume that every single human would accept his lack of perfect control over invisible biological agents, and refuse to order his brethren to wear flimsy pieces of paper over their faces to “protect others.” When even a 17-week Antarctic quarantine cannot do the job of stopping viruses, clearly isolating all children inside a six-foot bubble is counterproductive and silly.

The paper discusses the phenomenon of viral persistence in animals and humans (where it was previously known in children but not adults), and suggests the revival was possibly triggered by a cold snap. Unfortunately, the actual virus or other agent could not be isolated from the preserved samples.

Rudin has some less than nice things to say about Neil Ferguson, though she's far from the first, and only praise for Sweden, which she describes as our persecuted control group in the great experiment of running around like superstitious pigeons in masks. Most notable among her observations, though, are the perverse incentives for politicians to exacerbate their health theater efforts with no regard for the ultimate consequences.

Day 162: The One Percent

The US has made a couple of coronavirus records recently: yesterday was our first day with 70,000 cases, and today we hit 3.35 million cases total, which comes out to slightly more than 10,000 cases per million people. In other words, 1% of the population has been infected.

Elsewhere in the world, Argentina recently crossed the China line. Next in the queue is Egypt, with only a couple of days to go. Although Brazil is only racking up about half our daily case count at the moment, their daily deaths are well in excess of ours. In France, bus driver Philippe Monguillot, who was left brain-dead after an attack by fare-evading passengers he'd confronted for not wearing masks has died. While the Anglophone press has focused on the mask-evasion, the French press notes the fare evasion, and the prosecutors have called the five suspects "down and out drug users".

In the US, Texas seems to have pulled ahead of Florida despite a slightly lower average rate of cases. Georgia pulled ahead of Massachusetts yesterday, pushing us down to #9. (Our cases are up a quarter of a percentage point today). Pennsylvania at #10 is creeping towards the 100,000 case mark.

On the research (and weird symptoms) front, the Lancet reports a case of Kawasaki-like multisystem inflammatory syndrome in a 45-year-old man with coronavirus, "similar to what has been reported in children."

Although the cause of Kawasaki disease remains unknown, the most widely accepted theory is an aberrant immune response to an infectious trigger. Emerging reports depict the phenotype of MIS-C [multisystem inflammatory syndrome in children] as a combination of Kawasaki disease, toxic shock syndrome, and macrophage activation syndrome (or haemophagocytic lymphohistiocytosis), all syndromes of dysregulated immune responses. Our patient's presentation also included features typical of these different multisystem inflammatory syndromes.

The Conversation has a readable (if rambling) overview of the 20% ceiling of coronavirus infections, whether it represents a much lower threshold of herd immunity than the standard estimates (yes, if you're lucky), and what might be causing it (T-cell mediated immunity, either new or lingering from previous coronaviruses).

Day 161: Stolen Corona

The Federalist reports on an alleged coronavirus faker, Dr. Joseph Fair, a science contributor to NBC News. The notion that he faked a hospitalization for clicks is somewhat far-fetched, as is the idea that all his coronavirus symptoms were actually something else, merely because he has never tested positive for COVID-19, either by PCR or in later antibody tests. Nevertheless, failing to test positive for an actual case of COVID-19 is far more frequent than faking hospitalization or misdiagnosis.

Vox talks a bit about the testing situation from a more numerate perspective.

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

Day 160 Retrospective: Positivity in Massachusetts

The intertubes have been reconnected to PlagueBlog Headquarters, so we can upload our surprisingly large cities and towns maps again. For the week of July 8th, there were subtle changes to the MDPH's PDF that threw R for a bit of a loop, plus an intentional change to the percent positivity reporting: it is now averaged over the past two weeks rather than reported for the week in question. It's unclear whether this was just an impromptu smoothing effort, or was prompted in some way by the ongoing drop in positive tests. The drop is real, though; all positivity rates are below 12% and most are under 5%.

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

Day 159: Attrition in the Ranks

PlagueBlog headquarters is experiencing an internet outage, so reporting may be erratic for a few days. Today we leave you with yet another question about unworkable coronavirus restrictions in the schools: who's going to babysit educate your children from six feet away or online? Time reports on how coronavirus is thinning the ranks of teachers across the country. In one poll, "20% of teachers said they aren’t likely to return to teaching if schools reopen in the fall," a number that's close to the 18% of teachers who are 55 or older. (Some states reported even higher numbers considering bailing.)

The Centers for Disease Control and Prevention (CDC) recommends that schools space desks six feet apart; seat only one child per row on school buses; discourage students from sharing toys, books or sports equipment; close communal spaces, such as cafeterias and playgrounds; and create staggered drop-off and pick-up schedules to limit contact between large groups of students and parents. On Wednesday, Trump said he disagreed with the CDC’s “very tough & expensive guidelines for opening schools. While they want them open, they are asking schools to do very impractical things.”

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

Day 158: Justiça Poética

On the world stage, the top four players remain the same: the US, Brazil, India, and Russia. The US hit three million cases yesterday. Today's title was inspired by news that Brazilian President Jair Bolsonaro tested positive for coronavirus yesterday, showing mild symptoms and starting on hydroxychloroquine. Reuters has also reported the story (though also in Portuguese), which should make it into the Anglophone press soon enough. Apparently Bolsonaro has requested a recount, and new test results are expected today.

Peru has exceeded all versions of Spain's case count to take over the #5 slot a few days back, and Chile made a similar leap over the país natal today. Holding at #8 is the UK, where COVID survivor Prime Minister Boris Johnson has made waves allegedly blaming the care homes for deaths caused by poor COVID-19 control, when his government sent in untested patients a la Governor Cuomo. Number 10 has insisted Johnson's comments were not accusatory but merely a commentary on the consequences of the poor initial understanding of the coronavirus situation.

Next up at #9 is Mexico, an extremely strong performer in case counts despite minimal testing. Iran is at #10. Other big movers in the top 20 are #12 Pakistan, #13 Saudi Arabia, #15 South Africa (which just hit the 200,000 point yesterday with almost 9,000 cases in one day), #17 Bangladesh, and #19 Columbia.

In the US, Texas and Florida are struggling over the #3 and #4 spots, while a few more days of cases should put Arizona at #7 and push Massachusetts down to #8. The New York Times, quoting former city employee Frank Braconi, calls coronavirus a 'heart attack' for the NYC economy. The state has gone into 3.4 billion dollars of debt with the federal government after exhausting its own unemployment reserves in the economic crisis, and many companies remain closed or have already gone out of business.

Here in Massachusetts, The Hill reports that Governor Baker is letting us all vote by mail in both the primaries and the general election this fall. Also, a healthy smoothie shop owner in Plymouth is suing the governor in federal district court over his face mask requirement. She sounds pretty level-headed, but so far the news hasn't gone into the legal merits of her case.

P.S. Massachusetts cases are up a fifth of a percentage point today.

P.P.S. Fox News reports Trump's official withdrawal from the WHO effective July 2021. PlagueBlog notes that his threat to do so predates the WHO's silent admission at the end of June that they learned about the coronavirus epidemic from the Internet, and not from required reporting by China as they had long claimed.

Day 157: RIP Nick Cordero

Broadway actor Nick Cordero died Sunday after more than three months in the hospital. He was initially admitted for pneumonia, then diagnosed with COVID-19. PlagueBlog believes he would have been better off sticking with the pneumonia diagnosis, because most of his coronavirus "complications" seem to have been complications of mechanical ventilation. He was only 41, and no underlying conditions or unusual coronavirus symptoms seem to have been reported in his case; under today's less invasive standard of care he might have survived. People's report focuses on his devotedly optimistic wife (also a Broadway actress) and one-year-old son, rather than on the medical details of his case.

The pubs opened up again in Britain on this "Super" Saturday. Many journalists' hands were wrung over the dearth of masks and general holiday attitude, but the police found it a relatively calm night.

On the silly connections front, Fox News reports on the death of a man from an apparently famous 9/11 photograph from coronavirus. At age 60, Stephen Cooper was never in the towers, but was told by police to run away as he approached them with a delivery, and was photographed in flight. He later saw the photo for the first time in Time Magazine. When he died in late March, he was 78 years old, ill, and living in Florida, where his case of coronavirus was initially misdiagnosed as chronic obstructive pulmonary disease due to the lack of cases and testing there at the time.

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

Day 156: Is it Airborne?

Not surprisingly, the New York Times takes the climate-science might-makes-right approach with an article aptly titled 239 Experts With 1 Big Claim: The Coronavirus Is Airborne:

Most of these experts [interviewed by the NYT] praised W.H.O. staff for holding daily briefings and tirelessly answering questions about the pandemic.

But the infection prevention and control committee in particular, experts said, is bound by a rigid and overly medicalized view of scientific evidence, is slow and risk-averse in updating its guidance and allows a few conservative voices to shout down dissent.

PlagueBlog interprets "overly medicalized" to mean "only concerned about actual routes of transmission and not the fantasies of physicists and people who want to move the goalposts on the word airborne".

Nevertheless, the article is useful for its swift digression from science-by-mob-rule into the "precautionary principle," which seems to be the main point of contention in most fights over coronavirus, from the most minor and silly inconveniences involving silverware in partly-open restaurants up to the most economy-destroying and famine-producing acts of government.

While the Fourth of July merely suffered from coronavirus restrictions, the next national holiday has been cancelled outright: 7-Eleven will not be holding Free Slurpee Day on July 11th as planned. Even though the PlagueBlog staff have never celebrated Free Slurpee Day, we assure you that their plans to donate free meals and issue free slurpee coupons through their app is in no way an adequate substitute for this vital national holiday.

Massachusetts cases are up an eighth of a percentage point today.

Day 155: Bonfires and Illuminations

If John Adams could see us now...he might note our ongoing handwringing over some uniquely modest and non-threatening Fourth of July celebrations. The cause would probably puzzle him, as there was only a fifth of a percentage point increase in cases of a not particularly deadly disease here in Massachusetts today. At least he would be spared any reports of hand sanitizer-induced fireworks accidents.

Day 154: 11 Million Strong

The world has hit eleven million cases. The US is keeping ahead of Brazil despite the latter’s best efforts. Sonoma, Mexico has closed the border with Arizona over the US surge.

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

Have a happy Fourth of July. PlagueBlog advises against blowing yourself up with illegal fireworks, but scare stories about lighting your hands on fire due to the unlikely combination of fireworks and hand sanitizer are probably overblown, as it were.

Day 153: Bitter Roots

"The roots of education are bitter, but the fruit is sweet." Aristotle

Difficult as it is for the unpaid PlagueBlog staff to muster up any sympathy for a full-time food blogger who's wealthy enough to live in New York City and still pay the nanny for the past four months of non-work (even after her husband was laid off), Deb Perelman has a point about the infeasibility of some back-to-school social distancing plans. In NYC apparently this involves the kids physically attending school for only one week out of three. The rest of the time, it's your spawn, your problem.

At the same time, many adults — at least the lucky ones that have held onto their jobs — are supposed to be back at work as the economy reopens. What is confusing to me is that these two plans are moving forward apace without any consideration of the working parents who will be ground up in the gears when they collide.

Let me say the quiet part loud: In the Covid-19 economy, you’re allowed only a kid or a job.

She's not alone in her my spawn, your problem complaints. FSU, the Florida university famous for killing passing drivers with overwrought and under-engineered concrete pedestrian bridges, warned staff this week that "[e]ffective, August 7, 2020, the University will return to normal policy and will no longer allow employees to care for children while working remotely."

It's not just NYC backing off on public education as reliable childcare. The Massachusetts guidelines [PDF] are vaguer, with a lot of mask, hand-washing, and spacing requirements but no official decision yet on whether the school year will happen at school, at home, or in a "hybrid" format of alternate weeks in school and at home. Connecticut's plans are similarly vague yet difficult to implement. None of the plans sound like much of an improvement educationally or socially over the kids just staying home. It's also unclear what happens to teachers with their own children under a hybrid or remote-learning plan.

Now imagine if this were a flu pandemic, and children were actually in significant danger from the disease. Would we escalate the current unworkable plans into a realm of pure fantasy? Time, sadly, will probably tell.

Much hay has been made over the 50,000 cases reported in the US yesterday. Bars have closed in south and central Michigan, and the entire state of Pennsylvania and most of Texas have gone under the mask, while some Palm Beach County (FL) residents are suing over a mask mandate. Florida has extended its eviction moratorium. Tracing efforts aren't going so well in New York, so they're trying subpoenas instead.

The MIT Technology Review takes on the question of why California has joined in the new outbreak despite its early anti-coronavirus success. The answer is mixed. While testing and tracing cases is still going well, the issues seem to be among low income essential workers, those experiencing lockdown exhaustion, prisoners, and, perhaps most notably for the situation across the Southwest, citizens returning from the coronaviral disaster area that is Mexico for treatment at home. The Wall Street Journal also tries their hand at the California question, but takes the usual blame-the-victim approach and concludes that they lifted their restrictions too soon and let their counties run too wild.

Cases in Massachusetts are up a sixth of a percentage point today. Governor Baker, satisfied that the partial indoor dining reopening hasn't infected us all, has announced that Massachusetts will be entering Phase 3 on Monday, with casinos, gyms, fitness centers, museums and small event venues allowed open (mostly at reduced occupancy). Phase 3 has a part 2 to come, and Phase 4 is impossibly far off, in which a vaccine (or something) permits the reopening of bars, nightclubs, and large event venues.

Day 152: The Restaurant at the End of the Pandemic

New York, the most immune state in the Union, has backed off on its dining-in plans for Monday, instead indefinitely postponing indoor dining. Indoor dining was also scheduled to begin today in New Jersey, but back on Monday the governor postponed it indefinitely, apparently in horror at some outdoor crowd scenes.

PlagueBlog notes that restaurants are not normally filled with crowds but instead admit patrons according to their seating capacity. Both governors cited the outbreaks in the South and West as being partly driven by indoor dining, though PlagueBlog failed to detect any science behind those statements.

To be fair, the governors of most of the affected states seem to agree, though they also blame bar openings, and California also blames an increase in social and family gatherings—which seem a more likely culprit than the more limited groups able to assemble in restaurants. In Texas, the opposition says bar lives matter.

Here in Massachusetts we've had indoor dining for over a week now with no surge in cases, even though we are not as immune as either NY or NJ. Our cases are up only a quarter of a percentage point today. The weekly data is pretty boring:

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Day 151: The Zombie Uprising

Massachusetts cases are up a tenth of a percent today, with no new deaths. In fact, we have -41 deaths due to yet another data correction. (Beware of zombies.) On the other hand, California had the most new deaths in the US today at a cool 100, and they are also leading in new cases (over 7,000). Rhode Island remains the leader in testing, having managed to test more than a fifth of their population. New York is second at about a fifth.

On the hydroxychloroquine front, a letter to the European Journal of Internal Medicine questions recent, negative results from the West from a Southern perspective:

The countries of the South use hydroxychloroquine and chloroquine on a massive scale, just as they used them before for malaria, or still use them now for systemic lupus erythematosus and rheumatic diseases. And, as more than 2 billion people at least have used this treatment, they have the greatest difficulty in believing that this product has become, by 2020, an extremely toxic product.

On the legal front, over 30 Texas bar owners are suing the state over the bar closure. A US District Court also summarily granted a preliminary injunction against Governor Cuomo's unconstitutionally arbitrary suppression of religious gatherings (at 25% occupancy as compared to at least 50% occupancy for every other possible activity in the state).

Apparently you can't get interfacing for love or a reasonable amount of money these days, because it's all gone into masks [YouTube]. PlagueBlog must ask, is it really life without adequate supplies of interfacing, yeast, toilet paper and Chlorox wipes? More seriously, Lionel Shriver asks, Is living without risk really living at all?

Perhaps in future we’ll adulate a whole different set of national heroes. We’ll give Olympic medals to gymnasts who realise that flipping around uneven parallel bars is terribly dangerous, and so have prudently sat out their athletic careers in a chair. The winner of the Tour de France will be the cyclist who never rides faster than eight miles an hour and remembers to wear sunscreen. We’ll award the Victoria Cross to the safest member of the armed forces ‘in the presence of the enemy’ — who comes under bombardment and hides in the boot of his jeep, or who safely joins the other side if it seems to be winning.

Day 150: The Second Wave

PlagueBlog has learned (via Reddit) that people in air-conditioning-dependent places don't realize how many of us do without. So the AC theory of the second American wave of coronavirus may not be obvious to those chilling in their central AC in the midst of it. On the other hand, it's not obvious to Europeans just how much the weather and the accommodations to it vary across the US.

To be brief, central AC is much more common in the South and West than in the Northeast or Northwest of the US. Some have explained the current surge in the US by the summer flight into air-conditioning. Though herd immunity could explain the current state of the Northeast, it can't explain the largely-unaffected Northwest.

The Harvard Gazette chimes in on the dangers of air conditioning:

“The states that, in June, are already using a lot of air conditioning because of high temperatures are also the places where there’s been greater increases in spread of COVID-19, suggesting more time indoors as temperatures rise,” Nardell said. “The same [thing] happens in wintertime, with more time indoors.”

Professor Nardell implies that the theory relies on some airborne transmission of coronavirus, but it's not clear why it would when wintertime contagion is not contingent on airborne (non-droplet) transmission. Perhaps there are just too many Texans infected for droplets to have done it absent winter weather.

Also joining in on the second wave (though probably not on account of air conditioning) is the Brazilian city of Belo Horizonte, capital of Minas Gerais. They closed non-essential businesses back on the 8th of April, relaxed their restrictions on the 25th of May, and today re-closed-up shop. What qualifies as essencial is always interesting; in Belo Horizonte paint shops, lumber mills, and lottery kiosks will remain open. Bakeries get to open at 5am rather than keep the standard hours of 7am to 9pm. Oddly enough, banks are included among the essential businesses that have no restrictions on the hours they can keep, along with the more standard exceptions of pharmacies and gas stations.

Massachusetts cases were up a tenth of a percentage point today. We are currently patting ourselves on the back for being one of four states that seem to have nearly recovered from the pandemic. (Who the other three are seems to depend on who's counting.)

Day 149: Hyperventilation

Another one of the unknown knowns of coronavirus was the advisability of mechanical ventilation for serious cases. Back in May, Kit Knightly documented the lack of science behind mechanically ventilating persons suffering from respiratory diseases, as well as the poor outcomes:

Perhaps it is not surprising, then, that according to this [Associated Press] article 66% of UK Covid19 patients put on ventilators are dying. A recent study found that, in New York, 88% of ventilated Covid patients died. In Italy it was over 81%, in Wuhan it was 86%.

He traces this unknown known back to WHO guidelines about the possibility of aerosolization of the virus during non-mechanical ventilation and oxygenation procedures, which presumably must take place more frequently per patient than intubation for mechanical ventilation.

This leaves wide open the possibility that hospitals are using treatments known to cause harm, simply to avoid the hypothetical spread of the virus.

Fortunately, the medical response has backed off of mechanical ventilation. PlagueBlog blames panic and the lack of any useful treatment for the disease for the initial choice to repeat a pattern had already failed in Wuhan, rather than the WHO's advice per se.

There's some new math out in preprint today: Predicting the Trajectory of Any COVID19 Epidemic From the Best Straight Line by Michael Levitt, Andrea Scaiewicz, and Francesco Zonta.

It is evident from our data analysis that the growth of a COVID19 epidemic does not follow an exponential growth law even in the very first days, but instead its growth is slowing down exponentially with time. While all growth functions decelerate exponentially when approaching the plateau, the Gompertz function is unique in that it is decelerating from the first day, and thus can fit the first part of the COVID-19 outbreak.

Why that's happening is another question, one they waffle a bit on answering. It could be asymptomatic spread depressing the numbers, network (superspreader) effects, or it could be that this sort of thing just happens:

The existence of invisible cases of individuals who are mildly symptomatic and, therefore, not counted as confirmed cases may explain the non-exponential behavior of COVID-19: the known cases cannot easily find people to infect as the hidden invisible cases have already infected them. We realize that other factors may limit growth. For example, the structure of the human interaction network can lead to sub-exponential growth (Moreno 2002). Still, we believe that as SARS-CoV-2 is so infectious, it does not have a problem finding people to infect early on due to the local network structure.

Initial sub-exponential growth is not a unique feature of COVID-19, but has been observed in previous viral outbreaks and needs to be taken into account to produce accurate predictions (Chowell 2016).

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

P.S. In a published letter against intubation from earlier this month, A plea for avoiding systematic intubation in severely hypoxemic patients with COVID-19-associated respiratory failure, the authors confirm some of the suspected concerns mentioned above:

However, we reconsidered in other patients the rationale behind these early intubations and revisited the initial proposal of avoiding high flow oxygen in hypoxemic patients. In addition, we felt that the actual consequences of aerosolization posed by HFNC and NIV remain quite hypothetical as reported in H1N1 pneumonia. Our main concern was that a systematic intubation of every hypoxemic patient may prove to be untenable, facing a limitation of capacity and resources of intensive care units (ICU) to safely maintain a high number of patients on mechanical ventilation during the expected surge.

Day 148: The Unknown Knowns

The worldwide case count has reached 10 million, with 500,000 deaths. The US contributed significantly, as did India, which is still on the rise. Columbia recently passed the China mark, which only gets it to #21 these days. In the US, California surpassed New Jersey almost a week ago now, and Texas jumped past Illinois sometime yesterday. Massachusetts continues to rest on our antibodies at #7, with a third of a percentage point rise in cases today.

The governor of Florida wins Zinger of the Year with his response to the tri-state area's resolution to quarantine Floridians: he requests that Governor Cuomo "not quarantine any Floridians in nursing homes."

PlagueBlog readers may recall this famous Donald Rumsfeld quote:

Reports that say that something hasn't happened are always interesting to me, because as we know, there are known knowns; there are things we know we know. We also know there are known unknowns; that is to say we know there are some things we do not know. But there are also unknown unknowns—the ones we don't know we don't know. And if one looks throughout the history of our country and other free countries, it is the latter category that tend to be the difficult ones.

But there's a fourth category, which Rumsfeld also addressed:

At the beginning of the documentary, Rumsfeld argues that a major purpose of the Department of Defense is to evaluate "unknown knowns," or "the things you think you know, that it turns out you did not," to anticipate hostile actions before they take place. Illustrating his point, Rumsfeld suggests that the failure of the United States to anticipate the attack on Pearl Harbor was a failure of imagination.

The history of coronavirus seems to PlagueBlog to be an ongoing tragedy of unknown knowns. Though the science tells us we don't know whether masks, or even lockdowns, work at all, the general public is absolutely certain they do, to the point of blaming the victim (today I think it's Florida) for allegedly not doing those things, or doing them but not doing them religiously enough.

Scientifically, we don't know how many people have been infected or when it happened. (It may have all peaked well before the lockdowns and the months of enforced inactivity.) But people are so certain that coronavirus happens in lockstep with testing numbers, that things are still not back to normal even in New York City—probably the most immune place on the face of the earth after Wuhan and Lombardy. It's like a society-wide Dunning-Kruger effect.

Josh Ketter has a couple of articles on Medium chock full of unknown knowns. But we're not so good with the known knowns, either. People go on ignoring some fairly hoary science about viral respiratory diseases, in favor of paranoia about marathon-running virus particles (usually hallucinated by physicists) that have never been known to infect anyone. We know the math of a fraction of ongoing infection in the Northeast making it even more unlikely that that passing jogger could possibly infect you even if he stopped and spoke to you for 15 minutes, never mind just through the already-unproven route of exhaling outdoors. We know it's summer and going to a sunny, humid beach is not going to produce any significant level of respiratory illness, but Florida is still shutting down beaches like they're the problem.

Day 147: Is it the Air-Conditioning?

The US has reached 2.5 million cases, with 126,000 dead and a million recovered. While summer is being kind to the hard-hit Northeast, things are not going so well in warmer places. California, once a coronavirus success story, has surpassed 200,000 cases. The ICUs of Texas are upon the news, as is the situation in Arizona and Florida. While many other states are also on the rise, none of them, not even CA/TX/AZ/FL, are anywhere near the case rate or death rate of previously hard-hit states.

Everyone has noted the lower ages and milder disease progress of the disease in the currently surging states. The usual reaction is, nevertheless, to blame the victim-states for insufficient social distancing and mask-wearing (wholly independently of any statistical evidence of such) and the federal government for policies that have not changed much yet somehow managed to selectively slay old New Yorkers in the spring and hospitalize young Houstonians in the summer. Setting aside for the moment the dangers of blaming victims for their failure to abstain from all human contact, PlagueBlog notes a disturbing lack of scientific curiosity about what's actually going on here.

Some have at least asked whether the retreat into air conditioning for the summer typical of the most affected states is as dangerous as working in a chilly meat-packing plant. NBC News answers this question with a firm no:

But experts say there’s little evidence to link air conditioning to the spread of the coronavirus. Rather, the risk more likely comes from the amount of time spent indoors in close proximity to others.

“The opening up of facilities from my point of view, and I think this is shared by colleagues, that doesn't depend on the air conditioning, it's the gathering of the people for long periods of time,” said Dr. William Schaffner, a professor of preventive medicine and infectious diseases at the Vanderbilt University Medical Center.

“You can think of laboratory experiments and theoretical possibilities of how air conditioning might spread this virus, but so far, there really isn't any noteworthy evidence that this is happening,” he said.

PlagueBlog believes the clues are all there in the case rates. It seems you cannot hide from an uncured respiratory disease forever; it's not clear that you can hide at all. Maybe all you can do is pretend that your mild winter weather is actually an amazing success story for the half-hearted lockdown measures that it turns out you can't actually lift without having an eventual resurgence of cases—because your numbers were all the luck of the superspreaders and the weather to begin with.

That is, the only way to herd immunity is herd immunity, and some of us are already there because our weather was too cold or our superspreaders too super to successfully hide from the flu a coronavirus. Those who aren't there yet are now or will soon be facing the same old choice of trying to slow the virus down enough to preserve emergency room capacity, or not. (PlagueBlog does not recommend slowing it down until it's winter again, since summer COVID-19 outcomes seem to be much better so far.) On the bright side, it doesn't seem to take all that much herd immunity to knock the virus out; according to this May preprint, 10–20% immunity may be enough to do it.

Massachusetts cases are up a fifth of a percentage point again today. The New York Times article on the final report about the Holyoke Soldiers Home is at once damning and confusing. While it's clearer what went wrong, why is still a mystery; who gave the crazy orders and what they possibly could have been thinking or trying to accomplish with them remains unclear.

Day 146: Because Lying to the Public Went So Well the First Time

It's summer and the CDC has come out of its hole to tell some more howlers. In a surprise move, they removed being over 65 from the list of high risk factors, even though 80% of US deaths have been in those over 65. Since that's also the case for the flu, we'll give them a pass on that one, even though technically it means that all the killing-grandma panic has been, shall we say, somewhat misplaced. (That is, you were already killing grandma when you let the flu rip through society unimpeded.)

Perhaps most notably, they lowered their threshold for high risk from obesity from a BMI of 40 (morbidly obese) to a BMI of 30 (obese). Though to be honest, PlagueBlog hadn't even noticed their previous stance was so extreme (they went down two obesity classes, BMI 40+ and 35–40), because the science has always been behind class I obesity (BMI 30–35) already being a significant risk factor.

The remaining high-risk list is unobjectionable: "people with chronic kidney disease, chronic inflammatory lung disease, obesity, serious heart conditions, sickle cell disease, Type 2 diabetes, and weakened immune systems because of organ transplants."

Next, despite six months of accumulated science about COVID-19, they get to the howler: some people who "may" be at high risk. It's a long list of people, some of whom are at lower risk than the average person: smokers and pregnant women. Many studies have shown the prophylactic effect of smoking against COVID-19; that the CDC would invert this result and claim smokers are may be a high risk group is hurting PlagueBlog's ears with the howler.

It also casts doubt on the rest of the "may be high risk" list: undifferentiated asthma sufferers, those with liver disease or thalassemia, the demented, the lung-damaged, the otherwise immune-compromised, and those with "diseases that affect blood flow to the brain". The only ones who clearly belong on a high risk list are the Type I diabetics and those with high blood pressure (who appear on such lists often enough that it's unclear why the CDC is waffling here).

As for the "may be high risk" to pregnant women, the CDC cites their own report, even though it shows the opposite result (emphasis added for your reading convenience):

Symptom status was reported for 65.2% of pregnant women and 90.0% of nonpregnant women; among those with symptom status reported, 97.1% of pregnant and 96.9% nonpregnant women reported being symptomatic. Symptomatic pregnant and nonpregnant women also reported similar frequencies of cough (51.8% versus 53.7%) and shortness of breath (30.1% versus 30.3%). Pregnant women less frequently reported headache (40.6% versus 52.2%), muscle aches (38.1% versus 47.2%), fever (34.3% versus 42.1%), chills (28.5% versus 35.6%), and diarrhea (14.3% versus 23.1%) than did nonpregnant women.

Data were available on presence and absence of underlying chronic conditions for 22.9% of pregnant women and 35.0% of nonpregnant women. Chronic lung disease (21.8% pregnant; 10.3% nonpregnant), diabetes mellitus (15.3% pregnant; 6.4% nonpregnant), and cardiovascular disease (14.0% pregnant; 7.1% nonpregnant) were the most commonly reported chronic conditions. Data were not available to distinguish whether chronic conditions were present before or associated with pregnancy (e.g., gestational diabetes or hypertensive disorders of pregnancy).

Hospitalization was reported by a substantially higher percentage of pregnant women (31.5%) than nonpregnant women (5.8%) (Table 2). Data were not available to distinguish hospitalization for COVID-19–related circumstances (e.g., worsening respiratory status) from hospital admission for pregnancy-related treatment or procedures (e.g., delivery). Pregnant women were admitted more frequently to the ICU (1.5%) than were nonpregnant women (0.9%). Similarly, 0.5% of pregnant women required mechanical ventilation compared with 0.3% of nonpregnant women. [...]

No difference in the risk for death between pregnant and nonpregnant women was found (aRR = 0.9, 95% CI = 0.5–1.5).

PlagueBlog is hard-pressed to believe a story of disease progress in which pregnancy produces fewer initial coronavirus symptoms yet requires more medical treatment, and then, at the very point of mechanical ventilation, somehow saves pregnant women from (excess) actual deaths. Instead, PlagueBlog recalls the utility of death, the great equalizer, in showing the real COVID-19 status of a nation or a group. In this case, it appears that pregnant women are receiving a different standard of care than non-pregnant women (partly because pregnancy attracts extra medical attention even in the best of circumstances, not to mention the lack of accurate COVID vs. pregnancy data noted in bold above), but are otherwise just as young, healthy, and COVID-resistant as other women their age.

P.S. Massachusetts cases are up a fifth of a percentage point today.

Day 145: Houston, We Have a Problem

The world is at 9.5 million coronavirus cases. In the US, Texas and Florida are climbing by 5,000 cases a day. Florida has risen to #6 behind Texas, pushing Massachusetts down to #7. (Massachusetts cases are up only a sixth of a percentage point today.) While Arizona and some southern states are rising by 1,000–2,000 patients a day, but they're pretty far behind and won't be catching up to us soon.

Texas Medical Center in Houston is up to 97% ICU bed occupancy (from an average of 70–80%), and may run out of beds in a week or two. Texas Children's Hospital, also in Houston, is now taking adults on account of the coronavirus crisis.

New York, New Jersey, and Connecticut announced a joint requirement for travelers from particularly infectious states (Alabama, Arkansas, Arizona, Florida, North Carolina, South Carolina, Texas, Utah, and Washington) to self-quarantine for 14 days. In Massachusetts, we continue to merely recommend that all travelers from out of state self-quarantine for 14 days.

Also in Massachusetts, an Oxford gym owner who opened up on May 18th in defiance of the Commonwealth's ongoing gym closure and even remained open after the town cut off their electricity and water has finally been defeated because the owner of the building agreed to change the locks. PlagueBlog wonders what the state would have done if the gym owner had owned the building himself.

It's cities and towns day again today, and while things have well and truly flatlined (not even Fall River shows any notable activity), here are some maps for the record:

(Pop out.)

(Pop out.)

Day 144: The Real Surge

A new paper in Science Translational Medicine uses influenza-like illness (ILI) surveillance data to document an outsized epidemic surge in March in the US. [Paragraph breaks added for legibility.]

We identified excess ILI cases by first subtracting cases due to influenza and then subtracting the seasonal signal of non-influenza ILI (Fig. 1). Our approach identified known outbreaks of respiratory disease, including the recent outbreak of Respiratory Syncytial Virus that occurred in Washington state in December 2019. Starting in March of 2020, many states, including Washington, New York, Oregon, Pennsylvania, Maryland, Colorado, New Jersey, and Louisiana, showed a surge in number of non-influenza ILI cases in excess of seasonal norms.

For example, in the fourth week of March, 2020, New York State saw approximately 2 times higher non-influenza ILI than it had ever seen since the inception of the ILINet surveillance system within the US. We found that 10.2% of all outpatient visits in New York State during this time were for ILI that could not be explained by either influenza or the normal seasonal variation of respiratory pathogens (8.0% to 11.2% credible set).

As the seasonal surge of endemic non-influenza respiratory pathogens declined toward the later weeks in March, this excess ILI correlated more strongly with state-level patterns of newly confirmed COVID-19 cases, suggesting that this surge is a reflection of ILI due to SARS-CoV-2 (Pearson ρ>0.35 and p<0.05 for the last three weeks; fig. S2).

The US-wide ILI surge appeared to peak during the week starting on March 15 and subsequently decreased in numerous states the following week; notable exceptions are New York and New Jersey, two of the states that were the hardest hit by the epidemic, which had not started a decline by the week ending March 28.

Because they use all hospital visits as part of their ILI surge estimates, they go into some detail about how care-seeking and care-avoidance behavior (due to the growing fear of COVID-19, which would keep non-coronavirus-suspecting patients away but encourage coronavirus-suspecting patients to seek care) could have significantly affected their surge estimate. However, they conclude that non-care-seeking behavior for both mild ILI and non-ILIs cancelled each other out, leaving their original surge estimate intact.

Next up is consideration of mild and asymptomatic cases that would not have appeared in their surge estimates at all, leading them to the following conclusion:

Together these additional contributions from sub-clinical cases correspond to a mean clinical rate of 32% (the overall rate at which SARS-CoV-2 cases seek medical care) and a lower bound of 8.7 million SARS-CoV-2 infections between March 8th and March 28th (95% credible set 8.0 million to 9.4 million). Prevalence estimates for each state within this time-period are shown in fig. S4.

The figures, including the (tiny) state-by-state ILI graphs and that prevalence chart for the country, are in a separate PDF. For Massachusetts, they estimate prevalence at around 4%, making us #6 after NY, NJ, Louisiana, CT, and Maryland. (While all their data is state-based, it's not all labeled by state.)

Using deaths, they estimate a doubling rate in the last three weeks of March of 3 days, similar to the doubling rate of 2.65 days in Italy. They discuss various factors involved that could push the doubling time as high as 4 days, or lower it, including the lag time between the experience of symptoms and seeking care (and thus getting into the ILI surveillance system—4 days) and from seeking care to death (for their death estimates—11 days).

It's sort of a bright side that, in their estimation, the pandemic peaked for the US in mid to late March, and all the alleged peaking later was just about testing coming online as the disease itself petered out, either because of social distancing, advancing spring, COVID-19 having already consumed a large proportion of the susceptible population, or a combination of such factors.

On a different topic, PlagueBlog must note the loss of a popular science blog, Slate Star Codex, due to the New York Times' threat to doxx the author, who is a psychiatrist with various professional and personal reasons to want to maintain his anonymity:

When I expressed these fears to the reporter, he said that it was New York Times policy to include real names, and he couldn’t change that. After considering my options, I decided on the one you see now. If there’s no blog, there’s no story. Or at least the story will have to include some discussion of NYT’s strategy of doxxing random bloggers for clicks.

I want to make it clear that I’m not saying I believe I’m above news coverage, or that people shouldn’t be allowed to express their opinion of my blog. If someone wants to write a hit piece about me, whatever, that’s life. If someone thinks I am so egregious that I don’t deserve the mask of anonymity, then I guess they have to name me, the same way they name criminals and terrorists. This wasn’t that. By all indications, this was just going to be a nice piece saying I got some things about coronavirus right early on. Getting punished for my crimes would at least be predictable, but I am not willing to be punished for my virtues.

PlagueBlog will be replacing our previous SSC citations with archive.org links. Here's an archive link to all the coronavirus data and discussion that has been lost to the NYT's click-greed.

P.S. Massachusetts cases are up a fifth of a percentage point today. Also, the National Review reports on the Scott Alexander situation.

Day 143: Counterfeit Hand Sanitizer

The FDA has issued a warning about nine hand sanitizers made in Mexico by Eskbiochem SA de CV. They range from contaminated with methanol to wholly composed of methanol; some were not tested but appear to have been presumed guilty by association. (It seems even hand sanitizer can get cancelled.) Methanol does have legitimate topical uses, and PlagueBlog suspects that if a toxic topical dose were involved the FDA would have been more specific about the danger.

On the animal front, a preprint examining the susceptibility of pets, livestock, and wildlife has found, not surprisingly, that cats are particularly susceptible. Pangolins and hamsters are also known to become infected, and the authors cited a case of human-to-pig transmission. Despite that case and a perhaps unsurprising theoretical susceptibility, pigs proved difficult to infect in the lab. Poultry was particularly resistant, and the second most resistant was the dog. (Cabbits and mink were not mentioned in the paper.)

Mink continue to fall ill. The latest outbreak is on a mink farm in Denmark, where the Danish jumped immediately to the final solution of neovisicide. The count of concentration camps infected mink farms in the Netherlands has reached fifteen; it seems the Dutch government intends to slaughter them all (if it has not done so already). An animal rights group appealed the decision, but the judge ruled against the innocent, mostly-recovered mink.

Massachusetts cases are up 0.14% today. That's about 150 new cases, and not nearly enough to keep Florida (with 100,000 cases total) from passing us in just a few days. Georgia edged Maryland out of the top ten states yesterday.

Day 142: Nine Million Cases

The world hit 9 million cases today, with help from the ever-moving first wave in the US and new millionaire Brazil. Also of note is Qatar's recent jump past the China mark. Qatar is a small desert nation that, incidentally, does not happen to be the country of origin of coronavirus. Also, Qatar has approximately 1.4 billion fewer people than China does. PlagueBlog leaves it as an exercise for the reader to decide whether China's numbers remain believable or not.

RAND, however, does not leave the exercise to the reader. They estimate 37 times more cases in China than the official numbers, based on spread through air travel in early January. In other bad news for China, Beijing is up to 227 cases in their current outbreak, and a Chinese study has found some indications that antibodies to the milder Chinese coronavirus strain may not be effective against the European mutation known as D614G currently spreading in Beijing.

A interesting comment in Nature speculates that young and even middle-aged victims of severe COVID-19 may have succumbed due to genetic mutations to their immune systems. They go over some other possibilities as well.

On the mask front, Johns Hopkins has recommended the retraction of a paper in PNAS about airborne transmission:

This paper had two primary conclusions, neither of which were supported by the evidence presented. First, the authors concluded that mask mandates were the only factor that led to departures from the linear trend of case counts in Italy and New York City, and by implication, that no other non-pharmaceutical interventions (e.g., social distancing policies) were effective. Second, the authors concluded that airborne transmission is the major driver of COVID-19 spread. There were no measures of uncertainty reported.

But the feel-good story of the day is the Los Angeles high school class that evaded coronavirus regulations by disguising a graduation celebration as a Black Lives Matter march.

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

Day 141: No Mask Day

No Mask Day would have passed us by as no more than an unnoticed domain (redirecting to an obscure FaceBook post), if not for a sort of reverse Streisand Effect where the pro-maskers at Scary Mommy thought reviewing the weak sauce that is mask science was somehow an effective debunking of No Mask Day and defense of mom, masks, and apple pie. (For baseball, masks, and apple pie, see this equally tendentious article in which Sports Illustrated does little more than recite raw case numbers from Georgia.)

It's also No Mask Day in Somerville, where the health department in the mayor's head has finally relented on the outdoors-everywhere mask requirement and gone back down to the statewide rule of wearing a mask outdoors only when you can't socially distance. PlagueBlog has seen a huge increase in the scoffing of the previous, crazier law recently, so maybe the mayor and his mental health department felt they needed to bow to the inevitable. Do note that Cambridge still has the more restrictive (and insanely detailed) rule, so exercise caution at the city line.

Elsewhere on the mask madness front, the Sacramento County sheriff's office will not be enforcing the governor's new mask mandate. They do intend to comply, so this appears to be a statement about the feasibility of policing mask use rather than an anti-mask tirade. Sheriffs in Tulare[, Modoc,] and Orange counties have made similar statements; as one might expect for that hotbed of anti-masking, Orange County's was the most aggressive.

There have been a lot of strange theories (e.g., BCG vaccine), symptoms (e.g., COVID toes) and susceptibilities (e.g., type I diabetes) associated with coronavirus, but I think this particular high-risk group takes the cake: bald men. A paper in the Journal of the American Academy of Dermatology documents the Gabrin sign, i.e., androgenetic alopecia or baldness, named after Dr. Frank Gabrin, the first American physician to die of COVID-19.

To extend a previous study of the same issue, a bunch of dermatologists assisting in the coronavirus crisis in several Spanish hospitals documented patients' level of baldness on admission for three weeks. (The only standard was hospitalization.) Of those seen, 42% of the women and 79% of the men suffered from alopecia. They estimated the population average was less than or equal to 38% for women and 31%–53% for males. They did no analysis of the significance of this finding, instead soldiering right on to their recommendations for anti-androgen therapy (though the rationale behind this approach is left to the reader to figure out from the references).

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

Day 140: Rise of the Masks

Although the weak science behind masks hasn't changed any over the past week, the protests have proven virally harmless, the weather is improving, and American coronavirus numbers are flatlining at about a 1% rise a day, several states and jurisdictions have nevertheless jumped on the mask requirement bandwagon in the past day or so.

Most notably, the entire state of California is now under the mask. (The link is well worth a click for the photo of Governor Newsom touching his ersatz mask as he's holding it below his nose.) Despite the usual confused reporting, the new mask requirement there does not require masks outdoors when you can socially distance instead. PlagueBlog expects some pushback from uppity counties that refused the mask before.

If you read the tea leaves just the right way, the governor of Texas is now allowing local jurisdictions to require the mask. So far Bexar County (including San Antonio) and the mayor of Austin are on the bandwagon, and Houston is making noises about jumping aboard as well.

Yesterday in Florida, the mayor of Tampa announced a mask order starting at 5pm today. (Her faith in masks appearing out of the ether is touching, but does not take into account shipping times.) Miami-Dade already had a mask ordinance, which is now facing a legal challenge.

On the international front, Spain has been withholding its death count for about two weeks now, due to an alleged review of the provincial numbers and death dates that the government seems incapable of actually completing. PlagueBlog readers will recall this is not Spain's first bout of fudging the numbers, having previously dropped tens of thousands of positive antibody test results from their official total.

In Russia, a Stalinist Orthodox priest and his armed congregants have somehow seized a convent, apparently in retaliation for a church ban against his preaching that COVID-19 does not exist. He is holding services there at which one can, presumably, hear the forbidden sermons. He spent some time on YouTube before the occupation and is chock full of conspiracy theories, some of which sound much like ours (though without the involvement of Bill Gates). But other aspects of his position do not translate well—for example, his come-and-get-me defiance:

"You have the experience — you will have to kick us out from the monastery with police and national guard," he said. "I have a casket, I have a cross, I have nails — I'm awaiting your decision."

In Beijing, case counts from the wholesale market cluster continue to rise at what would be a rather lazy and negligible rate anywhere else. There, 183 cases counts as an "extremely severe" situation, even a wave, and is grounds for a "soft lockdown":

Now flights are being canceled, schools have been told to shut back down, and entire communities near the market, or with known COVID-19 cases, have been closed off and their residents barred from leaving. So far 29 neighborhoods have been completely fenced off.

Intercity travel has been largely suspended, especially outbound, and public facilities are limited to 30% of capacity.

Massachusetts' numbers will be out later today. While we've been creeping along, a couple of the hotspots have jumped past Pennsylvania. While Florida just made the leap yesterday, Texas is already on our heels and could surpass us today if they have a particularly bad day.

P.S. Globo reports that Brazil has hit a million cases. Also, the Boston Globe reports Governor Baker has announced that indoor dining can resume on Monday. Tables must be six feet apart and parties are limited to six persons.

P.P.S. Massachusetts cases are up a fifth of a percentage point today.

Day 139: Fire in the Hole

ProPublica condemns New York's policy of sending COVID-19 patients to nursing homes with numbers (plus a Cuomo quote about "fire through dry grass"):

In the weeks that followed the March 25 order, COVID-19 tore through New York state’s nursing facilities, killing more than 6,000 people — about 6% of its more than 100,000 nursing home residents. [...]

States that issued orders similar to Cuomo’s recorded comparably grim outcomes. Michigan lost 5% of roughly 38,000 nursing home residents to COVID-19 since the outbreak began. New Jersey lost 12% of its more than 43,000 residents.

In Florida, where such transfers were barred, just 1.6% of 73,000 nursing home residents died of the virus. California, after initially moving toward a policy like New York’s, quickly revised it. So far, it has lost 2% of its 103,000 nursing home residents.

PlagueBlog notes that the numbers would be more useful if we knew how much in excess of last year's nursing home deaths they were. People winter in Florida or move to sunny California for good reason. A redditor defends New York's policy and the inevitability of the outcome in a comment, noting that the harder-hit continental European countries experienced similar death rates (though the structure of nursing care is probably not directly comparable between Europe and the US).

Massachusetts cases are up a quarter of a percentage point again today. Here's a map of the current state of testing by city and town, from Wednesday's MDPH data. (Note that estimates of positivity rates have been calculated for the small towns that the state omits.)

(Pop out.)

Day 138: Brother, Can You Spare a Dime?

It's a sort of silly topic of the day, but the pandemic shortages have extended beyond PPE, toilet paper, hand sanitizer, yeast, and meat to the meta level: Reuters reports that the coronavirus has led to a shortage of American coinage. Between the slowdown in cash transactions and reduced production at the US Mint (both due to coronavirus), banks are running low on change.

Excitement about the cheap, generic steroid dexamethasone is finally dying down, perhaps because the real numbers are sinking in:

Dexamethasone reduced deaths by one-third in ventilated patients (rate ratio 0.65 [95% confidence interval 0.48 to 0.88]; p=0.0003) and by one fifth in other patients receiving oxygen only (0.80 [0.67 to 0.96]; p=0.0021). There was no benefit among those patients who did not require respiratory support (1.22 [0.86 to 1.75]; p=0.14).

Based on these results, 1 death would be prevented by treatment of around 8 ventilated patients or around 25 patients requiring oxygen alone.

It's somewhat depressing that this is the best showing for a drug after six months of pandemic, and that we only have it because some folks at Oxford decided to try out a steroid (among a bunch of other treatments), even though steroid use for ARDS was thought to be a fairly bad bet. But it's still better than nothing, and almost as cheap.

Massachusetts cases are up a quarter of a percent. Though some people are still holding their breath for protest repercussions, we seem to have escaped them. The statewide increase in cases for this week was only 1%, and the only major city with ongoing significant activity is Fall River, at 5% with 71 new cases for the week:

(Pop out.)

Day 137: The Salmon Panic

The case count in Beijing is now up to 106, with 8 more cases exported to a couple of other Chinese cities, all attributed to an outbreak at the Xinfadi wholesale market. Much of the capital has been locked down, and testing of about 300,000 residents and workers from the area is underway. China's chief epidemiologist noted that the cold, wet conditions of the wholesale market may have contributed to the outbreak (not unlike similar incidents in meat packing plants in the US, though he did not make that comparison).

Beijing's salmon panic happened a few days ago now, but it's one of those crazy coronavirus things that deserves a note in the historical record. The salmon in question was imported from Europe, as was the coronavirus strain behind the current Beijing outbreak, and chopped in a now-closed smaller market where a few cases were found along with the smoking SARS on the cutting boards. Yet coronavirus on food remains an unlikely route of contamination; it's far more likely that human beings carried the European strain into the wholesale markets than a boatload of dead fish did it. Nor does that reimportation need to have been recent (PlagueBlog has not seen the genetic analysis that traced it to Europe); the spikier Western strain of coronavirus has been on the rise worldwide for a while now.

Nevertheless, mostly harmless salmon was purged from the shelves of many Beijing grocery stores this weekend. PlagueBlog is not necessarily reassured that the Chinese people can still panic and do irrational things over a handful of cases, just like westerners. It seems innumeracy is still the biggest scourge of the pandemic.

A new paper in Physics of Fluids examines the droplets coming shooting out of and around surgical masks over time and "cough cycles". Ersatz masks are not considered, and N95 masks are mentioned mainly in the context of prior results, including this handy overview of ten other papers:

Previous studies report limited effectiveness in using surgical masks to reduce respiratory illness, and clinical trials report little effect on infection rates with and without surgical masks. In contrast, laboratory studies concerning coughing and infectious subjects showed that surgical masks are effective at reducing the emission of large droplets and minimizing the lateral dispersion of droplets. However, they allowed simultaneous displacement of aerosol emission upward and downward from the mask. Several randomized trials have not found statistical differences in the effectiveness of surgical masks vs N95 filtering face-piece respirators (FFRs) at reducing respiratory diseases for healthcare workers.

While the physics is interesting, the conclusions are somewhat more optimistic than they ought to be, considering that the paper considers the many routes of particles out of masks but not their relative infectiousness compared to unmasked droplets. If the masks were helping as much as the physics says, one would have expected better results on the previous studies that did consider actual respiratory infection.

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