Day 121: Estrogen Again

PlagueBlog readers may recall some rather ill-thought-out attempts to make male coronavirus patient survival rates more like female ones by administering estrogen. Perhaps the publication of a different sort of estrogen result will dampen that enthusiasm: Understanding COVID-19: Digit ratio (2D:4D) and sex differences in national case fatality rates (in Early Human Development Volume 146, July 2020).

To make a long finger short, everyone tends to have slightly shorter index than ring fingers (as measured from the crease), but men's are proportionally shorter than women's, given them a lower 2D:4D ratio on average. This difference has previously been shown to result from exposure to testosterone or estrogen in the womb, and the effect is stronger for the right hand.

Digit ratio is perhaps most memorable for its erstwhile association with homosexuality. It seems to have held onto the correlation between low ratios (extra-short index fingers) and lesbianism, while the correlation between high ratios (unusually long index fingers) and male homosexuality is now in doubt. Digit ratio has also been connected to an assortment of personality traits as well as some sex-specific cancers. However, it does not correlate with adult testosterone levels. It is worth noting as well that cross-ethnic differences in digit ratios can be bigger than the male/female difference, though these differences are still thought to be genetic.

The latest correlation with digit ratio is, of course, COVID-19 outcomes. Sadly, the paper involves no direct measurements of patients. Rather, in the tradition of the not-so-well-received vaccine theories, the authors dig up mean national digit ratios for a host of nations and compare them to case fatality rates (CFR) by sex:

At the national level, high mean 2D:4D (indicating low prenatal testosterone/high prenatal estrogen) is associated with high CFRs and percent male mortality. At the individual level, high 2D:4D may be a risk factor for severity of COVID-19 in males. We speculate that male 2D:4D is a negative correlate for expression of the SARS-CoV2 receptor (ACE2).

ACE2 expression is associated with healthy sex hormone levels in either sex, and, while a route of entry for the virus, ACE2 is also a defense against it. The authors' reasoning on this point seems to rely on hypogonadism being an ongoing effect of high digit ratio in men, but it's not (yet another reason not to try to correct the problem of maleness in the ICU). Nevertheless their speculation about ACE2 or ACE2-analogue replacement therapy as a treatment for coronavirus is interesting.

Massachusetts case counts are up 0.7% today. There appears to be a growing inverse relationship between mask compliance and ambient temperature. (Lock up your grandmas, folks; it's summertime!)

Day 120: Hip Hip Heparin

Heparin seems to have become a standard treatment for ICU coronavirus cases without this result, but nevertheless a recent preprint found it reduced mortality among hospitalized patients in Spain. Though the preprint has its issues, heparin has been successful enough that it seems unlikely a more controlled study will come along to clear things up.

On the historical front, the CDC has released some interesting Evidence for Limited Early Spread of COVID-19 Within the United States, January–February 2020, including a brief phylogenetic analysis of the multiple introductions of the disease into the US. The negative results are particularly significant, considering that quite a few Americans deeply believe they had coronavirus in December or January, but the data doesn't seem to support such early spread:

Two influenza vaccine effectiveness study networks with sites in six states (Michigan, Pennsylvania, Tennessee, Texas, Washington, and Wisconsin)* retrospectively tested respiratory specimens from patients with acute respiratory disease for SARS-CoV-2 by RT-PCR. At the Washington site, none of the 497 specimens collected during January 19–February 24 tested positive; the first specimen that tested positive was collected on February 25. At the five other sites (Ann Arbor and Detroit, Michigan; Pittsburgh, Pennsylvania; Temple, Texas; Marshfield, Wisconsin; and Nashville, Tennessee), none of 2,620 samples collected during January 19–February 29 tested positive for SARS-CoV-2.

The New York Times has even more details of the viral genealogy work that has untangled the various introductions of COVID-19 from Wuhan into the US and Europe.

Massachusetts cases are up 0.8% today. PlagueBlog notes that the City of Somerville is still lying to residents about having a mask policy that matches the state's; wearing a mask in public is not required in Massachusetts unless you cannot socially distance, you are indoors at an essential business, or you are on shared transit.

Elsewhere on the mask front, the WHO is still anti-mask despite rumored changes to their website. ("As described above, the wide use of masks by healthy people in the community setting is not supported by current evidence and carries uncertainties and critical risks.") Finland's Health Ministry also came down on the anti-mask side, finding "minimal benefits" and non-minimal risks.

Day 119 Retrospective: More Plateau

On Friday the world hit six million cases of coronavirus. Massachusetts cases were up 0.7%, and The Hill reported that consumer spending had "plunged" by 13.6% in April, despite a 10.5% increase in personal income due to unemployment overcompensation plus stimulus checks. It had previously dropped 6.9% in March.

It turns out New York State was not alone in the brilliant idea of sending COVID-19 patients into nursing homes full of the most susceptible population of people since the native Americans met the smallpox virus. Apparently the NHS has been doing the same thing in Britain since the start of the pandemic there, and several other US states did it as well. The National Review accuses California, Michigan, New Jersey, and, of course, New York, based on varying amounts of evidence. Breitbart adds Pennsylvania to the hall of shame. According to the AARP, California backed down from whatever grandma-killing plans they briefly contemplated, as did Massachusetts.

PlagueBlog managed to extract some cities and towns data to make this week's version of the usual graph, though the new testing and positivity data isn't mapped yet. The upshot of the case counts is much like the previous week: some big-looking increases in small towns and some ongoing activity in the Worcester suburbs, but most of the action is in Southeastern Massachusetts, especially Somerset:

(Pop out.)

Day 118: Killed by the Common Cold

The world is at 5.825 million cases. Russia, at #3, is nearing 380,000 cases, and Brazil (#2) is approaching 415,000 cases. Can Brazil eventually steal our #1 spot? The population of Brazil is about two thirds that of the US, and it's about to be winter there. On the other hand, in tropical areas of Brazil the rainy season (which is their flu season) is ending now. Brazil ought to be approaching the "brick wall" that the pandemic seems to hit after about 70 days in every country, regardless of local lockdowns and social distancing practices, but the pattern doesn't seem to hold in the latest South American outbreaks (Brazil, Peru, and Chile). That is, there's no evidence of a peak around 35 days followed by a decline, perhaps because of the slow start to their local epidemics. So there's unknown potential there.

Here in the US (1.75 million cases), meteorological summer is days away, and we've also hit the brick wall. (You know you've hit the wall when #4 Illinois, of all places, qualifies to reopen.) There's also some news out of Florida about who was actually dying down there.

Details on 2,017 deaths from coronavirus in Florida were released Thursday, after a threat of legal action against the state by media organizations.

The reports, produced by county medical examiners, show the dead ranged in age from 26 to 104 and were predominantly elderly. A third of the victims were diabetic. Twenty-seven [1%] were under the age of 40, most suffering from preexisting health problems. [...] The most common was obesity, followed by diabetes and hypertension. Several had more than one of these.

On the common cold front, there's a pre-proof out from Cell with the rather uninformative title Targets of T cell responses to SARS-CoV-2 coronavirus in humans with COVID-19 disease and unexposed individuals [PDF]. Though mainly about their research into T-cell responses in milder cases of COVID-19, the paper also makes some interesting comparisons to similar cross-reactivity research into the 2009 H1N1 influenza pandemic. Though the text is pretty opaque as these things go, this line from the summary says a lot:

Importantly, we detected SARS-CoV-2−reactive CD4⁺ T cells in ~40-60% of unexposed individuals, suggesting cross-reactive T cell recognition between circulating ‘common cold’ coronaviruses and SARS-CoV-2.

What this actually means is that the brick wall may, in fact, be herd immunity provided by previous exposure to other coronaviruses. Also the great mystery of different pandemic outcomes in different countries may have far more to do with circulating cold strains than with the severity of your lockdown or more exotic theories like off-target vaccination protection.

The Blaze reports on the implications of this paper:

On the one hand, this virus seems to be extremely contagious and transmissible. On the other hand, it appears to have been around for a while, possibly in December, and didn't kill too many people until super-spreading events in March.

On the one hand, the virus seems to kill a lot of vulnerable people for several weeks. But then it peaks after six weeks or so and nearly disappears a month or so later. We've seen the same curve in every country, almost as if it hits a brick wall and then runs out of steam.

[...] Perhaps, it could also explain why there appears to be a massive gap in severity of the virus in Asia vs. Western countries. Asian countries are regularly exposed to coronaviruses.

P.S. Massachusetts cases were up 0.7% today—not exactly grounds for cancelling the Boston Marathon (previously postponed to September), but they did it anyway.

Day 117: Because It Went So Well the Last Time

On the germ boat front, PlagueBlog is expecting some new entries from American Cruise Lines and American Queen Steamboat Company soon. These rival riverboat cruise companies making plans to start cruisin' for a COVIDding on June 28th and 29th, respectively.

Charles Robertson, ACL's CEO, said the riverboat operator is able to resume operations ahead of the cruise ships as capacity on most of their fleet's vessels falls under the 250-passenger limit covered by the Centers for Disease Control and Prevention's "no sail" order, which bars the big cruise ship operators from sailing until at least the end of July.

They're planning to reduce occupancy, and are also not expecting to fill up those first cruises.

Also on the let's try that again front, on Friday the CDC attempted to clarify the recent wording change to their coronavirus fomite advice that made an unexpected media splash a week ago now. Unfortunately their clarification isn't any clearer, nor does it give any references for the "old" science that makes fomites and singing Happy Birthday less significant than they were in the public mind:

CDC actively reviews our website to make sure the content is accessible and clear for all types of audiences. As a result of one such review, edits were made to the organization of the COVID-19 transmission page, including adding a headline in an attempt to clarify other types of spread beyond person to person. This change was intended to make it easier to read, and was not a result of any new science.

It's cities and towns day today, so watch this space for the latest plateau maps...

P.S. Massachusetts cases are up half a percent again today. Unfortunately, the promised improvements to the dashboard did not materialize, and instead the care facility information was taken out of the dashboard and put into the cities and towns data, which is now a massive PDF. At least the state bothered to put together some basic maps as part of the PDF (case counts, PCR test counts, and PCR positivity), and you will have to settle for those for the time being. The Boston Globe also has a basic map of case counts, with nicer colors but poorer scaling (and that's a hard bar to miss when it comes to the state's maps).

Day 116: Godwin's Law

Brazil surpassed Russia yesterday to earn the #2 slot. The UK is currently in the long penumbra of weird Spanish case reporting, where the real numbers make Spain #4 but Spain's artificially deflated numbers would make the UK #4. (Spanish case reporting in fact got weirder recently when Spain stopped disclosing its antibody test results at all, but Worldometers is still keeping track somehow.) Chile has surpassed Saudi Arabia on the way to China, and may even get there tomorrow.

The US is at 1.72 million cases with 100,000 deaths. The British press once again fails to resist a non-story about starving American rats. Back on Friday, California passed Massachusetts in cases to rob us of our #4 position. Next up is Pennsylvania, but they're still 20,000 cases behind. Then again, our cases are up only half a percentage point today, so even the most nominal of efforts would do it.

David Cole, amateur Holocaust historian and no stranger to Godwin's Law or purple pandemic prose, has brought Hitler and coronavirus together in his latest column, A Lockdown Line in the Sand. As late as May 1940, Cole recounts, Hitler and Himmler thought themselves above the notion of exterminating the ethnic minorities to the east. But over the next two years, times changed.

The Nazis did not go into World War II planning to break that taboo. They were hesitant, in fact, and that’s the point. They knew there was a taboo, they knew there was a line, and their first instinct was not to cross it. But eventually they did, and we have to ask ourselves, what did they gain? Did they win the war? In fact, not only did they not win, but Himmler would rather sheepishly concede in 1944 that they’d made a major oopsie by killing so many Jews in 1942 that they now needed to import Jews from Hungary to fill the labor vacuum left by the mass killings.

But what does Hitler have to do with a touch of the Wuhan flu? you might ask. Cole thinks the lockdowns crossed a similar, if less immediately deadly, line:

The most basic constitutional rights of worship and assembly (and other things the Founders didn’t think they’d have to enshrine, like the right to sit down and the right to leave one’s home barefaced) have been abrogated because some tin-pot state and local officials invoked the “cuz I sez so” rule. That’s a crossed line of dreadful magnitude. And just as with the Nazis, prior to crossing that line, the powers that be recognized the line, and respected it.

He continues with an informative history of how unthinkable quarantining the sick (never mind the well) really was, a mere five years ago—but only to reinforce the horror of our current state of rule by governors and uppity mayors instead of laws. Next time, he concludes, these thousand little cut-flower Stalins will act even more quickly to stomp on our faces and our rights.

Day 115: The Minks Go on the Attack

Reuters reports a second case of mink-to-human COVID-19 transmission on mink farms in the Netherlands. The first case was reported last week, in an employee who'd been working without PPE before the mink epidemic was detected. The human has since recovered, but genetic testing puts the direction of transmission from the mink to the human rather than vice versa (as was initially suspected). No details of the new case are available.

Cats appear to be the current suspect in the initial infection of the mink, as some of the farm cats were found to have antibodies already. Cats are no longer allowed near the mink, and minks on all farms are getting antibody testing.

On the unspeakable front, it seems that about 50% of all coronavirus deaths in Europe have occurred among nursing home residents. The numbers were crunched by the Japanese, who remain immune to most of our coronavirus taboos, but here are the numbers as translated by ProMED:

Country	Total deaths	Deaths in nursing homes	% of deaths in nursing homes	Most recent data	Source
France	28 239	14 363 (3713 died in hospital)	50.9%	18 May 2020	Public Health Bureau
Spain	27 709	18 413	66.45%	18 May 2020	Spanish Broadcasting Corporation
UK	31 855	11 687	36.70%	10 May 2020	National Bureaus of Statistics, etc.
Germany	7935	2980	37.56%	18 May 2020	Robert Koch Institute
Sweden	2075	948	45.60%	28 Apr 2020	Health and Welfare Agency
Italy	N/A	2724	N/A	14 Apr 2020	National Institutes of Health

Even more unspeakable is Jeffrey Tucker's article at the American Institute for Economic Research (AIER) claiming that the lockdown hasn't saved any lives, and we only tell ourselves that it did because of the sunk costs fallacy. He specifically cites fuller nursing home death data as part of his argument that locking down everyone was an expensive and counterproductive distraction from protecting those populations that were actually at risk.

Some of his data comes from the International Long Term Care Policy Network (latest data here), which finds that 41% of all COVID-19 deaths occurred in nursing home residents. A report on the available US data on Medium comes to a similar estimate of 42%, with a higher guess at 52% when excluding the outlier of New York.

It is true than any flattening of the curve before vaccines or effective treatments only saves non-COVID-19 patients from dying from lack of medical care in an overwhelmed system. It merely postpones actual coronavirus deaths, or possibly even increases them as potential patients age, sicken, fatten, and otherwise become more susceptible to the disease. (Presumably some of them would have survived an earlier bout of COVID-19.)

But without seeing next winter's coronavirus numbers, PlagueBlog would not jump to the same conclusion that none of our unused hospital capacity would have been used in the economically happier case of no lockdown. He does have a point about deaths resulting from the counterproductive drop in care as well as from the general deterioration of mental health under lockdown, but that seems to have had more to do with the general panic than with the government's role in locking people down per se. It's not so clear who is to blame for the panic—possibly social media qua virtual mob.

AIER is apparently based in Massachusetts, and dedicates an entire article to the Commonwealth as a cautionary tale of bureaucratic micromanagement demonstrating incompetence in the face of the Invisible Hand.

P.S. Massachusetts cases were up 0.64% today, and Middlesex County was up only half a percent. Needless to say, Phase 2 of our multi-phase micromanagement plan has not been declared yet. The Atlantic has an article on this disturbing lack of peakiness to the peak; apparently the Commonwealth is a microcosm of a national plateau phenomenon.

Day 114: A Nobel Prize in Coronavirus

Real numbers are leaking out of China again. National Review reports on a dataset from a Chinese military university leaked to 100Reporters almost two weeks ago, and reported at the time in Foreign Policy. Though the original reporters are withholding the actual data and did not speculate on totals, National Review does speculate that the data represents between 640,000 and 1.92 million cases, and that without covering the entire country or the entire duration of the epidemic. (If true, that would put China at either #1 or #2 in the rankings.)

On the Nobel Prize front, "Scott Alexander" has returned to the coronavirus well. The alleged lockdown seems to have made him punchier than usual:

It is the sixty-first day of shelter-in-place. Anti-lockdown protesters have stormed your state capitol, chanting Nazi, Communist, ISIS, and pro-Jeffrey Epstein slogans to help you figure out they’re the bad guys. Inside, the Governor has just finished announcing his 37 step plan to reopen the state over the next ten years. You kind of feel like he should be a little more proactive, but the protesters outside have just unfurled a Khmer Rouge flag, so you hold your tongue.

Eventually he gets serious and asks the Nobel-prize-winning question: why have outcomes varied so unpredictably from country to country? He begins his non-answer with a bunch of graphs showing that lockdowns do nothing—not because staying home is ineffective but because people were staying home anyway. He's not happy with this answer, but he doesn't have a better one.

PlagueBlog isn't happy with this answer, either. It would be much improved by the consideration that people were avoiding the actual dangerous situations: visiting elderly relatives (many of whom were locked down in institutions early on anyway), working from work, and holding large events, most of which were cancelled by antsy civilians before governments could shut them down. The lockdowns came later and did very little that was truly effective. How many people were ever having long, infectious conversations in small, non-essential retail shops? But, back to the unwon Nobel prize...

Scott Alexander is rather sanguine about how we're doing in the US:

America has one of the highest infection rates of any developed country, trailing only Spain. But it has one of the lowest mortality rates of any developed country, beaten only by Germany, Denmark, and a few other of the usual high performers. It’s right in the middle in terms of numbers of tests, beating eg Netherlands and Sweden, but trailing Germany and Denmark (though it may have an “advantage” on testing since so many people are infected).

Why we're doing so well is just another part of the prize-winning question. The best theory he has here is an addendum about age: the US does not have a particularly elderly population as compared to Western Europe. That a reader had to point that datum out to him in the comments is yet another sign of the age-of-death-denial phenomenon, as is the fact that a commenter had to debunk the 10 years of life papers for him (which of course PlagueBlog debunked for you a while back).

You've heard most of the theories he rates as weak here before: BCG vaccination, smoking rates, and strains of the virus. He doesn't go into detail about genetics as an explanation; once upon a time there was an Asians-have-more-ACE2 theory, but I doubt he meant that one. The post goes on to cover a bunch of other coronavirus-related topics because it's nominally a link post. If you need more random coronavirus facts it's a good place to go.

P.S. Massachusetts is up 1% again today.

P.P.S. Still reading the comments at Slate Star Codex, I found the best one of the entire thread, if not the entire pandemic (in response to the question, "Why is it called “novel” coronavirus?"):

Because it was the best of viruses, it was the worst of viruses, it was just the flu, it was a new Black Death, it was ushering in a new and better model for work and education, it was destroying the economy, it was inconsequential for the young, it was going to leave us all with permanent respiratory damage, it was imperative to trust the science, the data was all garbage and the models were worse, we would have a vaccine by the winter, we would never have a vaccine at all, we were all going direct to herd immunity, we were all going direct to the ICU – in short, the period was so far like the present period, that some of its noisiest authorities insisted on its being received, for good or for evil, in the superlative degree of comparison only.

Day 113: Waltzing Matilda

In a long-expected move, Canada progressed beyond the China point today, reaching thirteenth place among the nations at 83,000 cases. Though Saudi Arabia is next after China at #15, #16 Chile is moving the fastest of the under-83,000 crowd. Speaking of moving fast, Brazil added 20,000 cases today, leapfrogging over Russia to second place. Still, the US lead may be insurmountable at this point.

Legal challenges to lengthening lockdowns continue apace, most amusingly recall efforts against Governor Tim Waltz of Minnesota, perhaps inspired by his executive order [PDF] sharing the addresses of persons with positive COVID-19 test results with law enforcement.

A judge in downstate Illinois ruled Friday in favor of a tanning salon owner, issuing a temporary restraining order keeping his business open, but has not yet struck down the governor's stay at home order...yet. A state representative and several other businesses have also challenged the governor's orders; the governor is trying to move the representative's case to federal court, though it seems unlikely any federal law is applicable there.

Kansas lawmakers are moving to both sidestep the governor with the purpose of opening the state, and to bar certain lawsuits over coronavirus culpability. The actual list of the no-longer-culpable is somewhat unclear.

Massachusetts cases are up 1% again today.

Day 112: You Can't Handle the Truth

A scandal has been simmering for a while now about a New York state directive sending infected patients to nursing homes. The state has promised numbers, someday. The Associated Press got tired of waiting and counted for themselves, concluding that more than 4,300 COVID-19 patients were sent into nursing homes between March 25th and the governor's reversal of the order on May 10th. The governor now claims that nursing homes could have refused patients, although the directive said that they couldn't (at least until April 29th, when they were separately advised by the Health Department to reject new patients under certain circumstances).

The AP documents protests of this remarkably bad idea from the get go, but the governor's overriding concern seems to have been making space in the hospitals for more patients. That of course never precluded his current course of action (sending such patients to the overflow facilities), nor the obvious course of designating some facilities exclusively for infected patients (which other health care institutions have managed to pull off).

PlagueBlog wonders whether denial of the unspeakable truth that coronavirus almost always kills the old and unwell was the overriding factor in the stunning lack of clue necessary to send contagious coronavirus patients to nursing homes (many of which are also rehab facilities) chock full of the old and unwell. Yes, normally you'd send someone to a rehab after the hospital, but not if the direct result of doing so is going to be a vicious cycle of more hospitalizations and an unconscionable increase in deaths.

PlagueBlog also speculates that misinformation about the (virtually non-existent) risks of coronavirus to the young directly inspires conspiracy theories about the disease being a hoax, a side-effect of 5G towers, a globalist conspiracy to take away your rights, etc., etc. When you lie to people, they start wondering what the truth is, and when there's no obvious rational explanation, they seek out the irrational ones.

Massachusetts is up 1% again today. (This repetition in numbers is brought to you by the plateau and by PlagueBlog's rounding service.)

Day 111: Summer is Coming

Canada, at 80,000 cases, is creeping ever closer to the China mark. In the US (1.6 million cases), Illinois has exceeded 100,000 cases, and California seems to have exceeded the China mark yesterdayish. The New York Times is tracking which states have reopened (tl;dr: everyone except Illinois and NJ to some extent). Reuters reports that we're sending aid to Russia, most notably non-flammable ventilators.

On the semi-legal challenges front, the police chief of West Bolyston (a suburb of Worcester), has called the governor's business restrictions unconstitutional. He says he won't be enforcing them, and even made some recommendation to business owners about trespassing any Worcester health officials that come around complaining. Though the police chief didn't specify which constitution he meant, it is true that under the Commonwealth's, emergency situations are supposed to be handled with emergency laws approved by two-thirds of the state legislature, and nothing like that has happened yet. (If it ever does, such laws are applicable for up to a year, so it seems unlikely we'll get the 14-day out that Ohio did.)

A church in Mississippi was destroyed by arson yesterday, apparently in retaliation for having sued the city for their First Amendment rights. PlagueBlog is touched by the pastor's statement, "We don’t know anyone that we even think could be capable of doing something like this." It seems he hasn't been on the Internet lately.

On the weather front, a March paper in the Swiss Medical Weekly used the seasonal behavior of other coronaviruses to predict a sharp drop in COVID-19 cases over the summer followed by a new surge next winter. The Python code for their simulations is available at GitHub.

The CDC has decided that fomites are not a vector of coronavirus spread, which means you can now touch all that locked-up playground equipment pet stray animals, and you don't have to sing Happy Birthday anymore, if you were doing that. (Suckers!) Sadly, there are no footnotes on the CDC's COVID-19 page, so we don't know where this result is coming from.

P.S. Massachusetts is up 1% again today, though to more than 90,000 cases.

Day 110: The Five Million Mark

The world has reached five million cases. The US has 1.59 million of them, with Russia in second place at 309,000 and Brazil jumping to third place with 293,000 cases. Massachusetts is up 1% again today. Things are pretty calm on day 2 1/2 of Phase 1, except for some sour grapes among the pro-extreme-masking party over some stating of the obvious by the Plainville police department.

In a FaceBook post that survives only in reposts, they appear to have explained why they can't arrest non-mask-wearers: anyone can have a medical excuse and they aren't required to explain it. Apparently you can even have a mental health excuse. Perhaps the latter classification fits PlagueBlog's pre-existing condition of numeracy better. Believe me, it can be an extremely painful condition, especially in these trying times.

Also on the semi-legal front, a judge in Ohio has ruled that Ohio state law does not permit banning healthy people from going to the gym because somebody else has the flu a serious pandemic disease. Setting aside the question of whether it's legitimate to quarantine every single citizen of the state on suspicion of coronavirus, the judge noted that you only get to quarantine your suspects for 14 days, and those 14 days were up about six weeks ago.

It's cities and towns day here in Massachusetts, and the plateau plateaus on. Today's hotspots are all tiny towns where a few cases have an outsized effect. Out of the major cities, Fall River and New Bedford are the warmest compared to the rest of the state.

(Pop out.)

Day 109: You Can't Handle the Flu

The Spain issue arises again, as news outlets attempt to claim Brazil has reached third place in the coronavirus rankings. But for those who count all tested Spanish cases, not just PCR-tested ones, Spain is still at #3 with 278,000 cases compared to Brazil's 271,000. (Brazil should level up tomorrow at the rate they're going.) Russia remains at #2 with as close to 300,000 cases as makes no difference. The US retains the lead with 1.57 million cases.

While no nations have exceeded China lately, PlagueBlog notes that Massachusetts, at 87,000 cases, recently exceeded China's current count of 84,000 cases. (We exceeded China's death toll some time ago.) CNN notes that the Navajo nation has exceeded New York State's infection rate, with 2,304 cases per 100,000 (still using old census data) versus 1,806 cases.

On the somehow-not-the-flu front, a Washington Post article put forth the strange notion that we should suddenly, after thousands of years, start mourning victims of disease as though this were a new, surprising, and meaningful way to die instead of one of the most pedestrian causes of death known to man. PlagueBlog is tempted to remind WaPo of the 500,000 or so flu deaths worldwide that we brush off every year, but instead I'll let some "trusted sources" make the unspeakable comparison for me:

The New York Post reported on the summer of '69, when people cowered in their houses and wore masks crowded together barefaced in the mud at Woodstock, because the Hong Kong flu had been ravaging the land that winter and was looking to do it again the next winter. The article gets into the weeds after that, though it does let slip a couple of reasonably coherent theories about why people back then brushed off a flu pandemic on the scale of our coronavirus pandemic: one, men were real men a belief that challenges were good for your immune system, not something to run away and hide from, and two, an optimistic attitude about the potential of science to triumph over disease.

The New York Times has also taken on our international flu legacy, reflecting on the almost universal lack of memorials to the Spanish flu that killed upwards of a hundred million people worldwide. They do come to the conclusion that men were real men back then and they didn't want to think about embarrassing deaths from pneumonia in hospital, but noble deaths from mustard gas in the trenches. Or something like that.

Massachusetts is up 1% today, our first full day of Phase 1. Middlesex County is up only 0.8%, and Somerville, never a hotspot of the county, is at this very moment cancelling most of Phase 1 because the mayor and the health department in his head think it's too dangerous for someone from a young, healthy, and well-to-do community to get a haircut in the city rather than in one of the many saner cities conveniently located within walking distance.

Day 108: Massachusetts Reopens

The governor announced our reopening plan this morning. As usual, things are a bit contradictory: even though he extended the lockdown to today (May 18th), the plan for Phase 1 has certain businesses opening today. PlagueBlog cannot advise you which one is actually true. Phase 1 also reopens firearm retailers, even though a federal judge already reopened our firearm retailers over a week ago.

Phase 1 ("Start") seems to consist of three sub-phases, starting today, May 25th, and June 1st, respectively. Today's phase mainly opens up non-essential manufacturing and construction. (Construction in particular has been a confusing area all along, with some scofflaws and some voluntary unnecessary suspension, along with the usual uppity mayors making local rules.) To keep the feds at bay (or perhaps because he's a Republican and actually cares), the governor also reopened churches starting today. Some non-emergency medical care will be included.

May 25th is the big day when both you and your pet can finally get a haircut. Labs and offices can also partially reopen next Monday, and non-essential retail curbside pickup (including recreational pot and libraries) will be allowed. More non-emergency medical care will be allowed. Beaches, parks, drive-ins and some other outdoor locations will be partly reopened on the 25th. The third June 1st sub-phase is only about Boston; offices can't open until then in the city. Group gathering (less than 10 people) and hotel regulations (essential workers only) will remain unchanged until Phase 2, and some toothless advisory about self-quarantining for 14 days if you enter the state also remains in effect.

Phase 2 ("Cautious") has not actually been scheduled; it will happen after at least three weeks of Phase 1 depending on the numbers. On that happy unnamed day, we will be able to get our nails done, go inside non-essential stores and restaurants (apparently with occupancy restrictions), go camping, play unorganized sports, go to day camp, and use hotels (with unspecified restrictions).

Phase 3 ("Vigilant") has not been scheduled either and is even vaguer. Gyms and bars (but not nightclubs) will reopen then. Away camps and most tourist activity will also resume. (The cruise industry falls under federal restrictions.) Phase 4 ("New normal") involves the reopening of nightclubs and large venues. The biggest hole in the whole plan is the absence of any much mention of child care reopening dates, or of any legal protections for employees who cannot return to their now permitted jobs on account of the lack of childcare. [There is some rather unattractive option to send your children to the emergency childcare facilities, but only if you're not working from home.]

P.S. The state numbers were late today. We were up 1%, with some layout changes to the dashboard.

Day 107: Jab the Children

As predicted, Russia made its move to #2 today with 281,000 cases, outnumbering Spain's by any accounting. Canada at 77,000 is the next up to surpass China. The US is at 1.5 million cases and almost 91,000 deaths. Here in Massachusetts we're up 1%, and surprisingly, California at 80,000 cases is looking like a contender to catch up to our 86,000 cases and push us back down to #5, a spot we haven't seen in a long time.

A more general take on the measles theory from yesterday (and previous days) as well as its big brother the BCG theory, is that live vaccines of all sorts are generally protective against other diseases. One pro-MMR preprint suggests using MMR boosters to encourage the immune system to fight coronavirus:

We reason that children are protected against viral infections that induce sepsis because of more recent and frequent exposure to live attenuated vaccines (MMR, rotovirus, smallpox, chickenpox, BCG), which induce suppressive MDSCs [myeloid-derived suppressor cells] that limit inflammation and sepsis.

Strangely they don't mention MMRV (the newest thing in MMRs is to toss in some chickenpox along with the traditional measles, mumps, and rubella vaccinations), perhaps because neither a schedule nor a perceived need for boosting varicella immunity exists as of yet.

A letter to the editor of the International Journal of School Health last month also speculated on the protective powers of childhood vaccination, though they did not feel that the spike proteins of coronavirus and rubella (among others) were similar enough for a direct effect:

This [lack of similarity] suggests that memory T-cells, rather than vaccine neutralizing antibodies, may be involved in the protection of children against COVID-19. This is because children have a larger number of naive T-cells that can be programmed to protect them against the disease. This is consistent with a study in which the levels of SARS-CoV-2 specific antibodies correlated with age among 175 COVID-19 recovered patients. Elderly and middle-aged subjects developed higher levels of antibodies and lower blood lymphocyte counts compared to the younger patients. Meanwhile, no SARS-CoV-2 specific antibodies were detected in 6% of those younger than 40.

PlagueBlog found the recent spate of vaccine-related paper on Reddit, mostly thanks to user D-R-AZ. In the various discussion on Reddit it came up that infants under a year do not normally receive the MMR(V), and infants have also proven far more susceptible to COVID-19 than other young children (although, PlagueBlog must mention despite the taboo, such infant cases are still far rarer and far less dangerous than the flu).

Day 106: More Mediocre Measles Research

PlagueBlog readers may recall a paper from Day 71 about the MMR (and especially R) providing protection against coronavirus. It seemed weak at the time, but since then even weaker papers have come on the scene. The somewhat innumerate folks from Day 95 have since gotten their collection of anecdotes onto a preprint server, and another group has actually published a rather bare statement of the thesis in an open access, print-on-demand journal.

One interesting feature of the new paper is that, even more than the second one, they ignore rubella completely in favor of measles vaccination coverage. Their focus (if you can call it that) is on the structural similarities between coronaviruses and paramyxoviruses (both measles and mumps). They hit the high points: Italy has the poorest measles vaccination coverage (84%) in Europe, while China is on the ball at 97%, measles vaccination is associated with a drop in all cause mortality for the vaccinated, and cross-reactivity. But there are few hard numbers and no statistical analysis beyond these points.

The BCG school is much further along with the math, so far so that a group of epidemiology grad students have debunked one of the (many) papers making similar connections between tuberculosis vaccine and coronavirus. Sadly, the debunking is also short on math, only mentioning that perhaps new COVID-19 numbers would lead to different results, rather than actually crunching the latest batch in search of said different results. The debunkers also mistake the argument from cross-reactivity for some sort of "common sense" approach that can be dismissed with their own somehow more common common sense. Actually the protection some vaccines provide against unintended targets is a prior result, not an illicit truism.

In plague ship news, CNN reports that there have been eight relapses aboard Germ Boat #23, the USS Theodore Roosevelt. Like the later disowned South Korean relapses, all eight sailors tested negative twice before they were allowed back aboard and caught out in later testing.

In local news, Massachusetts cases are up 2% today. Although Middlesex County is up only 1% and Camberville have never been hotspots of the county despite their density, the City of Somerville has cancelled all fun through next December—most notably HONK! and the annual Fluff Festival. (Fluff is from Somerville.)

Day 105: The Governor Cancels Monday

In a surprise move, Peru joined India in the Great Leap Forward to the wrong side of China. Russia is edging ever closer to #2; one bad day could put them there, and two average days are sure to do it. Italy's death count currently stands at 31,614, only notable because...

The Istituto Superiore di Sanità has put out a report on 27,955 coronavirus deaths in Italy (circa May 7th), finding a mean age of death of 80 and median of 81 (85 in women, 79 in men). They contrast this with the median age of infection, which was 62. They totaled up deaths for every decile, finding 3 below 10, none in their teens, 9 in their twenties, 54 in their thirties, 246 in their forties, almost a thousand in their 50's, almost 3,000 in their 60's, and then some very high numbers (7849 for the 70's and 11395 for the 80's), only dampened at the end by the general lack of nonagenarians in the population (only 4,430 died).

But wait, there's more! Only 4% of the dead suffered from no comorbidities, while 60% of them maxed out at 3 or more. (Some more breakdown would have been helpful there.) The most common comorbidity was hypertension (68% of deaths) followed by type II diabetes (31%), ischemic heart disease (28%), atrial fibrillation (22%), chronic renal failure (20%), and then COPD, heart failure, recent cancer, and dementia (all around 16%). Obesity and stroke followed (at around 11%), and they tracked five other conditions (all below 5% or so). They broke these down by sex, but the differences weren't large.

But wait, there's more! In 93% of hospitalized patients, symptoms were typical for COVID-19. The analysis of atypical symptoms is not particularly useful, but there is some data for time of stay. The median length of infection before hospitalization was 5 days, and the median length of hospital stay (until death) was also 5 days. ICU stays were 9 days long, but don't seem to have been very common considering the median without ICU remained at 5 days.

But wait, there's more! Only 312 deaths (1.1%) were of persons under 50, and only 66 of them were under 40. For those 66, comorbidity information was only available for 52, 40 of whom had "serious pre-existing pathologies (cardiovascular, renal, psychiatric pathologies, diabetes, obesity)".

No, there's no more. Here in Massachusetts our cases were up 1.5% today. The governor has extended the non-essential business ban for one day until Tuesday, filling in the legal loophole (at least for Monday).

P.S. For comparison, our average age of death in Massachusetts is 82.

Day 104: Doctors without Filters

The world stands at 4.5 million cases and 303,000 deaths, with Russia still chugging along at 10,000 cases a day in its quest for Spain's second place seat. India is very close to exceeding China, despite China's renewed testing in Wuhan after new cases were reported there.

Things are fairly calm in the US, with active cases flattening out. Though Illinois is looking a bit hot, it's too far behind New Jersey to catch up anytime soon. Massachusetts cases are up 2% today. The governor still doesn't seem to get that his order closing non-essential businesses expires on May 18th and everything legally reopens, unless he explicitly orders otherwise—not just hems and haws about a report coming out after the fact.

PJ Media has picked up on an anti-mask opinion piece by a neurologist originally posted at Technocracy News. Since there are no studies of preventing the spread of COVID-19 with masks, his model for masking is the flu, but he cites a literature review showing no evidence that masks prevented flu transmission. PlagueBlog has seen similar studies discussed before, and one consistent problem with them is that they're mostly about masking the well, not the ill (never mind the allegedly invisibly ill).

However, he does cover the base of not masking the allegedly invisibly ill. He says any kind of mask, whether ersatz or professional quality (though it's worse with N95 masks), will concentrate virus from the breather and send it back into their respiratory tract. In the case of SARS-CoV-2, with its penchant for entering the brain through your nasal passages (knocking out your sense of smell on the way), the last thing you want to do for hours on end is snort it back up your nose.

Now that we have established that there is no scientific evidence necessitating the wearing of a face mask for prevention, are there dangers to wearing a face mask, especially for long periods? Several studies have indeed found significant problems with wearing such a mask. This can vary from headaches, to increased airway resistance, carbon dioxide accumulation, to hypoxia, all the way to serious life-threatening complications.

PlagueBlog was particularly impressed by the N95 mask-wearing driver who fainted from lack of oxygen and crashed his car. The author also expressed some serious concern for the elderly and ill restricting their own oxygen supply with masks. He concludes with the usual argument for establishing herd immunity instead, but PlagueBlog believes that herd immunity is the outcome of a particularly successful immunization program (such as we don't have for the flu), and not something you get by just throwing up your hands and letting 'er rip.

Day 103: Safer in Court

It's not just our economy that was unprepared for quarantining 330 million well people instead of 1.4 million sick people; our court system is also unaccustomed to the sudden closure of churches and other non-traditional responses to The Disease Which Shall Not Be Compared To The Flu. The economy is quick to fold under assault, while the court system lies low and considers its arguments. But once it rouses itself, hold on to your quarantine-the-well orders, folks, because it's going to be a bumpy ride.

Today, with the legislature egging it on, the state supreme court of Wisconsin struck down the governor's attempted extension of a "Safer at Home" order. It fell partly on technicalities of how and by whom it was done, but mostly on the law in Wisconsin not permitting the wholesale closure of the state (at least not in the chapters cited as a basis for doing so). The whole thing is 161 pages long if you want to take a look for yourself.

In other legal fights, the governor of Texas is at odds with San Antonio and other big cities over reopening. The state's main point of contention is (allegedly) unlawful local restrictions and/or fines exceeding the state's existing coronavirus regulations.

On the free exercise front (no, not jogging without a mask—the First Amendment), a US District Court has struck down the governor of Kentucky's attempt to ban in-person church services. Though it's the same state, it is not the same case as the sixth circuit court case unbanning drive-in church services.

Elon Musk says Tesla is suing Alameda County for, basically, not doing the corona the way Trump does it. There's also some incomprehensible lawsuit going on in Nevada over who can prescribe (hydroxy)chloroquine and where; at least one county has already tapped out.

Massachusetts cases are up about 1.5% today. Judging from the governor's daily presser, we little people don't get to find out which businesses are allowed to open back up on Monday until...Monday. Even if the owners somehow get more warning than the rest of us, that hardly sounds conducive to resuming business.

In any event, it's Cities and Towns day today, and here's a new map for you. Things are so plateaued that I had to change the percentile scale to make the tiny bit of variety more visible. The hottest new hotspot is Hamden down at the bottom of Hamden County, the only spot to go up more than 100% in the past week. But it was only 20 new cases; Connecticut probably wasn't wearing a mask one day and coughed on them.

P.S. Some adjustments for mobile have been made to the map (in place).

Day 102: The Minks Have It

Once again Russia is in the mixed news; by surpassing the UK in cases today, they have raised the question of whether they have achieved second place after the US, or remain in third place after Spain. As readers may recall from Day 90, Spain reports only cases with PCR testing in their case count, but the ranking sites include cases from antibody testing. (Note that probable but untested cases are not included at all, leading to some serious undercounting there.) This disparity has exceeded 40,000 cases at this point. That may sound like a lot, but Russia will probably have its #2 title in under a week regardless even if they keep on burning down ICUs with defective ventilators.

In late April two Dutch fur farms were quarantined due to coronavirus infection in the minks, which showed respiratory symptoms. Roadblocks were set up pending testing of air and dust samples at the farms. Although the two farms were relatively close together (six miles apart), the minks were suspected to have been infected by workers at the farms. Although it's unclear from the reports what species of mink is farmed there, it seems that the European mink (Mustela lutreola) is endangered and hard to breed in captivity, while the American mink (Neovison vison) is more amenable to farming and is probably the infected animal.

Minks are related to ferrets, which have previously been shown to be susceptible to COVID-19, though the American mink is more distant from the ferret than the European version. So it's not surprising that in the crowded conditions of a farm the virus is (apparently) passing from animal to animal. (If you feel sorry for the minks, don't worry; fur farming in Holland is scheduled to end in 2024.) In fact, ProMED noted a preprint from China that used deep learning algorithms to conclude that bat and mink were likely intermediate species for the transfer of SARS-CoV-2 to humans.

Last week two more Dutch mink farms were quarantined with similar outbreaks. Some pneumonia deaths among the affected minks have been observed. Since it is now mink breeding season, it has also been discovered that the disease especially affects pregnant minks (unlike pregnant humans). Rabbit farms are also being screened for coronavirus, but no results have been released thus far. While no evidence of the spread of coronavirus from mink to human has yet surfaced, PlagueBlog recommends caution when farming mink (which remains legal in the US).

In other animal news, a French cat was reported infected at the end of April, and a robotic dog from Boston Dynamics is herding people in Singapore.

PlagueBlog is going out on a limb here and predicting that the uptick in Massachusetts cases will be 1% again today.

Day 101: Don't Sue the Sioux

The world stands at about 4.24 million cases, with 286,000 deaths. Reporting is mixed on whether Russia has achieved third place yet, but according to Worldometers, it's still at 4th place with 2,000 more cases than #5 Italy and 2,000 less than the UK at #3. In a surprise move, India has surpassed Canada on the way to China; both of them and Peru are hovering around 70,000 cases.

In another surprise move, Illinois, with 79,000 cases, has finally deposed Massachusetts from our longstanding place at #3. (That's what we get for plateauing on at slightly less than a 1% increase in cases today.) Also, a couple of Sioux nations have gone full-on Rhode Island, setting up checkpoints on highways to protect themselves against coronavirus. Just like Cuomo threatening Rhode Island, Governor Noem of South Dakota has threatened to sue the Sioux. Since the tribes appear to be well within their rights on this one, state lawmakers are urging the obstinate governor not to throw money away suing the Sioux.

In other native news, Huffpost reports that the Navajo have edged out New York State for the title of most infected Americans per capita, with 1,786 cases per 100,000 versus New York's 1,751. However, Huffpost seems to have made the Navajo rate up out of 2010 census data, which is probably much more out-of-date than whatever the New York Times is using for their latest estimate of 1,760 cases per 100,000 in New York State. (Massachusetts is at 1,129, in case you're curious.)

Interlude: Mad Squirrel Disease

PlagueBlog apologizes for missing this 2018 account of a death from mad squirrel disease in Rochester, New York circa 2015. Mad squirrel disease (not its official name) has apparently been known for at least 35 years.

The risk of contracting Creutzfeldt-Jakob disease by eating squirrel brains was documented in the Lancet in 1997. It seems the skilled roadkill chefs of rural Kentucky are able to extract brains from squirrels (which is perhaps the most impressive part of the whole story), which they then scramble with eggs or add to a stew named "burgoo".

The Lancet article is still paywalled after a quarter of a century, but the New York Times reported on it at the time, giving away a good deal of paywalled information:

In the last four years, 11 cases of a human form of transmissible spongiform encephalopathy, called Creutzfeldt-Jakob disease, have been diagnosed in rural western Kentucky, said Dr. Erick Weisman, clinical director of the Neurobehavioral Institute in Hartford, Ky., where the patients were treated.

''All of them were squirrel-brain eaters,'' Dr. Weisman said. Of the 11 patients, at least 6 have died.

Within the small population of western Kentucky, the natural incidence of this disease should be one person getting it every 10 years or so, Dr. Weisman said. The appearance of this rare brain disease in so many people in just four years has taken scientists by surprise.

While the patients could have contracted the disease from eating beef and not squirrels, there has not been a single confirmed case of mad cow disease in the United States, Dr. Weisman said. Since every one of the 11 people with the disease ate squirrel brains, it seems prudent for people to avoid this practice until more is known, he said.

The journalists are also more specific about squirrel prep:

Families that eat brains follow only certain rituals. ''Someone comes by the house with just the head of a squirrel,'' Dr. Weisman said, ''and gives it to the matriarch of the family. She shaves the fur off the top of the head and fries the head whole. The skull is cracked open at the dinner table and the brains are sucked out.'' It is a gift-giving ritual. The second most popular way to prepare squirrel brains is to scramble them in white gravy, he said, or to scramble them with eggs. In each case, the walnut-sized skull is cracked open and the brains are scooped out for cooking.

These practices are not a matter of poverty, Dr. Berger said. People of all income levels eat squirrel brains in rural Kentucky and in other parts of the South. Dr. Frank Bastian, a neuropathologist at the University of South Alabama in Mobile, said he knew of similar cases of Creutzfeldt-Jakob disease in Alabama, Mississippi and West Virginia.

The self-styled "Official Mad Cow Disease Home Page" seems to have covered this story as well, even including a recipe for burgoo. Significantly for the timeline, they also included several references from the paper. Among them was a 1984 article, Creutzfeldt-Jakob Disease. Possible Transmission to Humans by Consumption of Wild Animal Brains, in which the wild animals considered were wild goats and squirrels.

And that's the smoking squirrel that takes us back 36 years, to a time long before mad cow disease. Needless to say, PlagueBlog recommends you remove and dispose of the brain and spinal cord before eating any mammal, whether it has been reported to transmit TSEs yet or not.

Day 100: Length of Stay and Years of Life Lost

It hasn't been a hundred days of solitude yet; the PlagueBlog count is rather of 100 days of infection in Massachusetts, since our first infected student arrived ex-Wuhan. In today's milestones, the US hit 80,000 deaths, and Massachusetts had only a 1% uptick in cases.

I was inspired by a comment to look into some real numbers for length of stay in nursing homes. Back in 2010, a paper in the Journal of the American Geriatrics Society pegged the median length of stay at 5 months, with 53% dying within six months. There's a long tail that makes the average length of stay more than a year, and a significant sex difference that makes the median only 3 months for men but 8 months for women. Surprisingly, chronic conditions were not a significant factor.

The numbers were even older than the paper, so I looked for some newer data, perhaps reflecting improvements in geriatric care. The closest thing I found was a more recent paper in the Journal of Post-Acute and Long-Term Care, but the numbers were not directly comparable. They considered only medicare patients entering nursing homes for the first time. Even with those restrictions, the median length of institutionalization was still about 5 months. While some patients were ultimately discharged (rather than dying in care or moving between hospitals, short-term care, and back to long-term care), they often died soon after discharge. The mortality rate over the course of the year after first admission was 35%. (Note that the admissions year they used was a fairly average flu season.)

If you compare the reality of nursing home care to some journalism out there about years of life lost (YLL), the numbers don't quite add up. Just for example, a study out of Scotland calculates YLL from the usual sorts of actuarial tables, which indeed indicate another 10 years of expected life for the elderly age groups most susceptible to coronavirus—on average. However, the life expectancy of persons already in nursing homes is somewhere around 14 months from admission, and usually less than that by the time they catch coronavirus. So where the actual YLL lies between 0.6 and 10 depends on how many victims are coming from nursing homes.

Numbers coming out of Europe estimate nursing ("care") home deaths at about 50% of coronavirus deaths overall. In the US, the picture is more complicated, but in leading states like New Jersey, Massachusetts, Connecticut, and Pennsylvania, well over 50% of deaths have occurred among nursing homes patients (plus some staff).

Day 99: Rhode Island Reopens

Rhode Island's restriction against non-essential businesses expired today. Though there are still mask and occupancy restrictions on businesses, the state was declared reopened in the news. But us increasingly shaggy Massachusetts neighbors should not get our hopes for haircuts up; as PlagueBlog readers may recall, there's still a 14-day quarantine required before out-of-staters can do anything worth doing in Rhode Island, like fish or golf.

It seems that golf courses were essential in Rhode Island all along, and only the recent, overly complicated Massachusetts golf exemption has led to a regulatory morass for the Pawtucket Country Club, a Rhode Island business with 15 1/2 holes located across the state line in Massachusetts. It goes without saying that only Rhode Islanders can play the 2 1/2 holes located in Rhode Island. There is no corresponding restriction in Massachusetts, so Rhode Islanders can play the whole course, but Massachusetts residents cannot (nor, presumably, can they use the Rhode Island-side clubhouse). Massachusetts does not permit the use of golf carts, so only Rhode Islanders can scoot around from hole to hole that way. The owner is concerned that this level of crazy will cause members to quit the club (and mowing all that lawn is apparently expensive, though essential enough on both sides of the state line).

We're up 2% again today in Massachusetts. Today was Couchfest in Somerville, the Porchfest replacement that involved a lot less crowding in front of porches blocking traffic to the sound of live music (actually, no traffic-blocking at all). In Boston the mayor cancelled all fun until through Labor Day.

Day 98: Depression Kills, Too

The world is quickly approaching 4 million coronavirus cases, with 273,000 dead and about 1.4 million recovered. Although the BBC has noted Italy's landmark of 30,000 dead, the UK is actually ahead of them with 31,000 deaths. The UK is also eyeing Italy's 3rd place position in cases, though with #5 Russia still shooting up at 10,000 cases a day, they may not hold it long. (The Russian case count does not include the mysterious rash of COVID-19 defenestrations among health care workers there.) Brazil has surpassed Turkey to gain the #8 slot; Reuters reports on ongoing concerns about undercounting there.

The US is at 1.3 million cases and 77,000 deaths. The pandemic may be plateauing, but the unemployment numbers are not. The Washington Post is particularly pessimistic about the numbers of people who will end up returning to work. Well Being Trust predicts [PDF] 27,644 to 154,037 "deaths of despair" in America as a result of the growing coronavirus recession, depending on how long it lasts. Their middle-of-the-road prediction is 68,000 deaths.

P.S. Massachusetts is up 2% again today. No more Walmarts have been lost to coronavirus, but our US Congressional critters are making their displeasure with the chain known nonetheless.

Day 97: Crying Wolf

Don't worry; I"m not going to talk about how it's still not the flu, or how unscientific restrictions on harmless, healthy fresh air do more harm than good. No, the crying of wolf came up in the news today when the governor felt the need to ask people to answer the phone when the COVID-19 tracers call. It seems that more than 50% of their calls go unanswered, even though the caller ID says MA Covid Team. Much like the press conference where he told people to go to the hospital if you're sick, he trotted out a bunch of community representatives to repeat the message that you should answer your phone when COVID calls.

The federal government should have done something about spam phone calls, say, five or ten years ago already, before they needed the phones for a pandemic response. You snooze, you lose your telecommunications channel to noise. PlagueBlog recommends that COVID leave voicemail, preferably in English. (Portuguese is an option, but Chinese is right out.)

Speaking of Massachusetts, our numbers are up 2% today. Our golf courses are open by special dispensation of the governor, but it's a complicated reopening because there are some rather unnecessary rules (considering the existing social distancing requirements), and they're still non-essential businesses so cannot have employees doing anything but required maintenance.

Wired reports on why it's so hard to pack meat without spreading a pandemic disease. Erin Bromage, a biology professor at UMass Dartmouth, also touched on the meat packing menace in her latest blog post, on the risks of reopening.

Day 96: Excess Deaths and Excess Walmarts

Massachusetts' cases are up 2.5% today, to 72,025 cases, 4,420 deaths, and a total of four Walmarts closed (in Avon, Abington, Quincy and Worcester). The New York Times reported on excess deaths across the country. Because of lag, they mainly consider late March and early April, during which we were up 24%. New York was at 323% and New Jersey at 90%, but otherwise excess mortality was mild at worst.

Today is cities and towns data day. With many thanks to the MDPH, below is an updated map (or open in a new tab). If you switch to the Increase map layer, you can see our plateau in all its beige glory. While there's still a bit of activity in the southeast, most spots of color on the map are either small towns or numbers that were revised down (shown in gray).

:

Day 95: More Retroactive Cases and Vaccines

The news has picked up on the 42-year-old Algerian man in Paris who was in the ICU on December 27th for what turned out to be COVID-19, a month before France's first two official cases (ex Wuhan) on January 24th. The patient, a fishmonger with pre-existing conditions, had not travelled since an August trip to Algeria, but tested positive on retroactive testing of stored samples and so is considered an instance of early community spread. He also had a child who suffered from an influenza-like illness (ILI) before he himself fell ill. Some news outlets have since reported that the man's wife worked with Chinese people at a supermarket near the airport.

A pre-proof of the associated paper is available at ScienceDirect: SARS-COV-2 was already spreading in France in late December 2019, in the International Journal of Antimicrobial Agents. Perhaps the most interesting thing about the paper is that the authors were not hunting very hard for cases; they were merely associated with a hospital in the north of Paris which routinely preserves respiratory samples. They restricted their testing to their own ICU patients between December 2nd and January 16th, for whom the medical record included both ILI and ground glass opacity on a lung scan, and a negative result for other infectious disease (flu, other coronaviruses, etc.). The paper was not clear on what the hospital routinely tests for.

This exclusion process left them with only 14 samples, of which only one tested positive (twice). They conclude that their restricted sample (especially the exclusion of all other infection, as co-infection with the flu and COVID-19 has been documented in China), and the possibility of false negatives (due to the test itself or damage to the samples in cold storage) may explain finding only one case when that case was clearly of community spread.

On the vaccine front, another group has made the MMR connection PlagueBlogged back on Day 71. Though it's a rather sketchy "report" from "World Organization", the anecdotes (PlagueBlog hesitates to call anything within "statistics") are interesting. They note that the US Navy routinely administers MRCV (an unspecified measles and rubella-containing vaccine chosen out of the options of MR, MMR, and MMRV, which contains chickenpox vaccine) to new sailors, possibly explaining the low death rate aboard navy plague ships. Besides their anecdotal evidence for several countries, they do provide some references for the MRCV coverage rates noted in their anecdotes, as well as citing the paper from last month [PDF]. An enterprising person might actually analyze the data and write an actual paper about it.

Without any statistics it's hard to make any falsifiable claims, yet they do get some things wrong. One of them is the likelihood of people over 60 having been vaccinated, a topic on which they are technically correct because of undue focus on MRCV (which includes a measles vaccine), but quite wrong when arguing the efficacy of rubella vaccine as they seem to be doing. Non-immune women of childbearing age have gotten vaccinated since the introduction of rubella vaccine in 1969; in fact the risk of birth defects from rubella (as vividly demonstrated by rubella epidemics in the 60's) was the main impetus behind the creation of the vaccine. Needless to say, many of those women are well over 60 now.

They're also doing a titer study of COVID-19 survivors; you can sign up online. Considering their general methodology it may never get published, but you can apparently get your titers back from them.

The case count in Massachusetts is up 1.7% today. In Middlesex County it is up only 1.4%. PlagueBlog advises Somerville residents not to listen to lies from the city about the governor's face mask requirement; as reported in all honest sources, Governor Baker has only required face masks outdoors and in other unspecified public places in cases where you cannot maintain social distancing. The specific requirements are also unchanged and involve only stores and shared or public transit. PlagueBlog also notes that this is the last day of the grace period on the $300 fines, and recommends you breathe free one last time.

Day 94: Still Not the Flu

Cases in Massachusetts are up only 1.5% today, though this may be lag from the weekend. Neither the state nor PlagueBlog is maintaining a 3-day running average of our numbers, but the New York Times has graphed our seven day average among plenty of other colorful stats.

For reasons that remain obscure to PlagueBlog, we are not supposed to compare COVID-19, a viral respiratory infection spread by droplets that tends to kill the elderly in large numbers mainly via the accompanying pneumonia, to the flu, a viral respiratory infection spread by droplets that tends to kill the elderly in large numbers mainly via the accompanying pneumonia. The Wall Street Journal didn't get the memo, and actually compared the two last month. Despite missing the memo, they managed to hit a bunch of the usual specious arguments without ever really answering the title question, Why Doesn’t Flu Tank Economy Like Covid-19?

PlagueBlog has a simple answer: because we're used to the flu. If you gave it a fake name and said it was going to kill 60,000 mostly old folks in the US this season, we might all freak out and shelter in place. But since it's been killing large quantities of people every year since before the Spanish flu, we give it a pass. This is not to say that we should tank the economy for the flu, too, or even that we shouldn't have done it for the coronavirus. PlagueBlog is just answering the WSJ's rhetorical question.

And, of course, PlagueBlog is willing to compare coronavirus to the flu. Some would say you cannot compare the two because we have a vaccine for the flu, but actually, the flu goes on killing the elderly in large numbers despite the vaccine, while, PlagueBlog hopes, COVID-19 will actually be stopped by a vaccine. (It seems one is not allowed to say the flu is worse than coronavirus, but one may say coronavirus is worse than the flu.)

Some would say you cannot compare COVID-19 to the flu because the death counts are vastly different. While it's true that the death counts are different, the difference is less than an order of magnitude. Coronavirus has already slightly exceeded a bad flu year in the US (69,000 vs. e.g., 61,100 in 2017–2018). The US is a heavily vaccinated country, but worldwide the flu is still well in the lead: recent estimates put the worldwide annual flu death toll at 291,000 to 646,000. The current coronavirus death toll is only 250,000, and while it seems likely to equal a mild flu year (especially considering undercounting of deaths), it's less likely to match the flu in a bad year.

Some have suggested that the number of low-grade and asymptomatic cases in the community matters somehow, especially (it seems) because we're having trouble detecting them for COVID-19. However, we have similar difficulties detecting low-grade and asymptomatic flu cases, which is why flu rates and deaths need to be modeled rather than simply counted outright. Due to the current intense interest, prospects are somewhat better for calculating IFR (infection fatality rate) for all conceivable cases of COVID-19, and this number will certainly be lower than the more useful CFR (case fatality rate), which at least tells you something about the chance a particular sick patient will survive the disease. However, PlagueBlog fails to see how this forthcoming low number will somehow lessen the impact of the actual deaths of the 250,000 dead victims of COVID-19.

Similarly, some claim that dying all together from COVID-19 in the first four months of the year is somehow different and worse than dying at a slower rate over the eight months of flu season. The one-time debut speed of COVID-19 does have some potential effect on the health care system and access for other patients. But, since we still don't have particularly good treatments for COVID-19 (that an infected patient might be missing out on due to rationing of health care), the speed of infection seems a minor issue compared to the absolute number of COVID deaths.

Some feel that the occasional deaths of young people from COVID-19 is somehow worse than the occasional deaths of young people from the flu. But the flu actually kills between ten thousand and a hundred thousand children under 5 each year, not to mention plenty of other young people at higher rates than COVID-19. PlagueBlog begs you to think of the children.

Day 93: Karma is a Bat

In today's numbers, the world has 3.54 million infected, with 247,000 deaths. Spain is approaching 250,000 cases, Italy has topped 210,000 cases, and the UK has attained 4th place with 186,000 cases. Russia is on the move with 134,000 cases, including over 10,000 in the past day. Brazil's burning rainforest approach to the virus has now pushed them past China to 97,000 cases, right on the heels of Iran.

The US is nearing 1.2 million cases, with over 68,000 dead. Worldometers is now breaking New Jersey and a few other states down by county, but not Massachusetts even though our data is available. (We are up 3% again today.)

On the karma front, China's policy of inveigle the world, infect the world doesn't seem to be paying off, with a crippled export industry showing "no sign of recovery." Also, a pair of honeymooners who somehow made their way to Hawaii have been jailed after violating the 14-day quarantine for out-of-state visitors by leaving their hotel room to get pizza. You can read the state's press release, "From the honeymoon suite to cell block", here, and the blow-by-blow of their violations here. Hawaii is ranked #47 out of the 50 states with only 620 cases, and they seem to intend to keep it that way.

PlagueBlog was never a fan of the L vs. S strain theory, and yet another paper is out debunking it: No evidence for distinct types in the evolution of SARS-CoV-2.

Day 92: The Germ Boats Strike Back

The Miami Herald is still on the plague ship watch, with the latest numbers and a google spreadsheet of their data. They also reported on the mysterious death Thursday of the senior doctor of the Norwegian Cruise Lines ship Norwegian Gem. Germ Boat #28 is currently off the Bahamas with only crew aboard. Dr. Alex Guevara died in his sleep of "cardio-respiratory arrest," but rumor has it that he was suffering from pneumonia at the time, and had been working with a nurse who tested positive.

The cruise line asserts without any evidence or testing that the doctor, who was treating crew with "respiratory illnesses", did not have COVID-19. They also asserted that the previous crew death aboard, of a 56-year-old Filipino man with tachycardia arrhythmia in mid-April, was not due to COVID-19 despite the lack of either testing or an autopsy. To add insult to injury, they also acted illegally in their handling of the single COVID-19 case that they have admitted among the crew of #28.

I found Germ Boat #29, the Celebrity Apex, in the Herald's data, but the Guardian has the most recent coverage of the world's newest plague ship. The ship was completed by Chantiers de l'Atlantique in Saint-Nazaire, France in early March. It appears to have been the first cruise ship ever delivered virtually (to Celebrity Cruises), due to coronavirus restrictions on travel at the time. While the planned inaugural ceremonies were soon postponed to a much later date, a crew of 1,407 was installed and a party was held in late March despite the French lockdown.

After a handful of early cases appeared, the crew was quarantined on the ship, which has apparently never left dock at Saint-Nazaire. Wikipedia has case numbers as of April 15th, at which point 224 people were positive out of 1444 tested. (The Guardian reports that two were still hospitalized and 700 trapped aboard at that time.) An infected crew member from Bulgaria who managed to escape and recover has since launched a class-action lawsuit against the cruise line in US district court.

On the drug front, a preprint from yesterday reports on the Broad-spectrum antiviral activity of naproxen: from Influenza A to SARS-CoV-2 Coronavirus, apparently by binding to the viral nucleocapsid protein. They both modeled this interaction and reproduced it in vitro, and are now working on a clinical trial. Rumors you may have heard earlier in the pandemic that NSAIDs were bad for you were baseless even at the time; the rumor-mongers seem to have backed off when the cytokine storms blew through.

Massachusetts is up 3% again today. Currently hospitalized and ICU cases have fallen. There have been no mask rebellions like the one in Stillwater, OK. PlagueBlog has already observed risk compensation (one of the many dangers of ersatz masks) among the masked masses.

Day 91: Snakes and Smokers

Massachusetts is up another "plateauing" 3% today. The governor, perhaps getting a bit annoyed at all the tin-pot mayors making up their own I-know-better-than-the-MDPH mask guidelines, has turned his CDC-based recommendation into a requirement, with fines. It's otherwise unchanged, though: you still don't need to wear a mask outdoors if you're able to socially distance, because the coronavirus is not some misunderstood medieval miasma. It's just a virus.

Believe it or not, today's title refers to a single, prepress paper at the open access journal Toxicology Reports: Editorial: Nicotine and SARS-CoV-2: COVID-19 may be a disease of the nicotinic cholinergic system. There's a lot of stuff going on in this paper (though no actual experiments), and to understand the relationship between snakes, smokers, and COVID-19, we need to back up a bit.

Back in the day when only East Asian men seemed to be catching the new coronavirus, there was a theory out there that their smoking habit (as well as their over-expression of ACE2) was part of the problem. (Smoking is known to increase susceptibility to other respiratory ailments.) But the numbers disagreed, as they so often do. Some authors of the current paper published several reports showing that smoking instead seemed to be protective, as did others including the CDC (although the CDC wasn't explicit about it, so you need to read the tea leaves of the linked table). The number of smokers hospitalized for COVID-19 has fallen far short of expectations, though it has been observed that once hospitalized (and thus, PlagueBlog postulates, deprived of their smokes), outcomes for smokers are poorer than average.

Why? you may ask. The paper posits the activity of nicotine as "an important inhibitor of pro-inflammatory cytokines acting through the cholinergic anti-inflammatory pathway". Moreover, because "the cholinergic anti-inflammatory system provides better control and modulation of the cytokine response compared to blocking a single [cytokine]," nicotine may actually be a better drug for the condition than several cytokine blockers currently being tested.

The paper also considers the ACE2 question. There have been conflicting studies over whether smoking and nicotine down-regulate or up-regulate ACE2, the later results being for up-regulation. While extra ACE2 was, like smoking, once thought to be a free ride for the virus into cells, more recent theories give extra ACE2 a positive role in continuing to perform its own functions after much ACE2 has been disabled by the virus. The paper also notes that up-regulated ACE2 is an advantage of estrogen and youth, and women and young people are known to have milder courses of disease.

There's a lot of (theoretical) mechanism of action in this paper, if you've been looking for some gory details of what SARS-CoV-2 is doing differently in the body than your average respiratory disease. The authors note that anosmia and its less-reported brother, ageusia (lack of the sense of taste) are signs of the virus attacking brain cells that happen to express ACE2, including, they postulate, the vagus nerve. The exact mechanism by which swelling of the vagus nerve affects the cholinergic pathway is not so clear from the paper, but apparently nicotine can still get through and do its anti-inflammatory magic.

And then, there were snakes. Why snakes?

As more studies presented the clinical manifestations, laboratory findings and disease progression in COVID-19 patients, it became apparent that the nicotinic cholinergic system could explain most (if not all) of the disease characteristics. It would be unlikely for a single “defence system” to ameliorate all the diverse and complex manifestations of COVID-19, unless that “defence mechanism” was the target of the viral host. Could that be possible?

[...] Taking into consideration that snake venom toxins are competitive antagonists of acetylcholine on α7-nACh receptor with high affinity, we decided to explore the hypothesis that SARS-CoV-2 may have acquired sequences by any of the potential, and not defined yet, intermediates through genomic recombination [on its way through a snake]. We compared the protein sequences between SARS-CoV-2 and snake venom neurotoxins. We were able to identify regions with four or five amino acids homology between the coronavirus and several neurotoxin molecules.

Though they're not very explicit about it, the authors do cite a paper that mentions snakes as a likely intermediate species that was also for sale at the Huanan Seafood Wholesale Market.

P.S. A redditor has collected vast quantities of SARS and COVID-19 smoking statistics.