Day 136: Riding the Second Wave

The world is at 8.1 million cases, with 439,000 dead. Massachusetts cases are up a tiny fraction of a percent today (0.082%), with still no wave of protest-COVID (because respiratory diseases do not spread easily outdoors, folks, no matter how much science you've forgotten or how afraid you happen to be). Nevertheless, you can get a free test for coronavirus from the state if you attended a protest.

While there has been a lot of worry about a second wave, actual full-fledged second waves are hard to come by, even in countries now entering winter. One country that's almost certainly on its second bout of coronavirus is Iran, which is peaking again after an initial high in early April. Mid-June has produced about 2500 cases a day and a death rate that has risen to over 100 a day. The main cause to doubt the wave is the long-term issue of generally unreliable data coming out of Iran, due to low testing rates and an abrupt stoppage of province-level reporting back in March "after hard-hit areas posted numbers that were multiples of official data."

Reuters reports another 40 cases in China, 27 of them in the Beijing outbreak. It's unclear how many of them are asymptomatic. The wetness of the wholesale market(s) at the center of the outbreak is also unclear, though ProMED reports at least one sold pangolin in the past.

On the news-unfit-to-print front, the Spectator picked up on Stanford professor John Ioannidis' impressively low estimates of the IFR (infection fatality rate) of COVID-19. They dared report it as being possibly lower than the respiratory disease that dare not speak its name flu. Also, another preprint is out on the protection smoking provides against coronavirus.

The FDA has revoked its emergency use authorization for hydroxychloroquine and chloroquine. The drugs remain approved for other uses in the US, and any physician can still prescribe them for an off-label use like COVID-19 prophylaxis or treatment. Whether anyone will is another question entirely.

Day 135: Domino Masks

While a domino mask may keep you safer than an ersatz mask (by concealing your identity from roving mask police while neither suffocating you nor giving you a false sense of security), today's title actually refers to a few more defeated mask rules, which PlagueBlog can only hope will trigger a chain of dominoes leaving only the sane and scientific social distancing rules in their wake. (One can dream.)

Back in May, Japan urged its citizens not to wear masks outdoors in hot weather to avoid heatstroke. Rather than heatstroke, summer weather in the US leads directly to mask rebellion, described in detail in the Washington Post.

Here in Massachusetts, mask rule overreach happens at the city level, but on the other side of the country, the Mercury News describes an even more divisive county-by-county saga of voluntary vs. mandatory mask wearing—one that drove an Orange County official out of her job and led to the reversal of their mask requirement after over a hundred residents complained:

Although she did not provide a reason for her resignation, Quick was receiving heightened security due to threats stemming from her mask order.

Protesters brought a poster with Quick’s photo embellished with a Hitler mustache and swastikas to a previous Board of Supervisors meeting.

Newsweek reports that Governor Doug Ducey of Arizona has declined to order mask wearing in the state, out of an excess of pragmatism:

"There's not a cure for this virus, and there's not a vaccine for this virus," the governor added. "So this virus is something we need to learn to live with, and we need to make sure that we are protecting the most vulnerable in our society."

(Hint: if you're in a grocery store doing your own shopping, you are unlikely to be "the most vulnerable in our society".)

Here in Massachusetts (where cases are up only a fifth of a percentage point), you can plead any unspecified medical condition and probably get out of wearing a mask, but in Singapore it seems you need to plead multiple personality disorder to escape the swinging cane of justice.

Day 134: Every Earth is Fit for Burial

Today's title is by Marlowe, and the news that inspired it came from Brazil and Indonesia. Brazil, long #2 in case count, exceeded the UK in deaths just yesterday, 42,000 to 41,000. (The US is still #1 at 117,000.) Even though the US has a higher case rate (6,474 per million) than any European country bigger than Luxembourg, our death rate (355 per million) remains much lower than that of European hotspots like Belgium (833), the UK (614), Spain (580), Italy (567), Sweden (483), and France (450). PlagueBlog thinks the occasional COVID-19 survivor getting a huge hospital bill he'll never actually pay is a small price to pay for a non-socialized healthcare system that saves almost twice as many lives.

The AP makes hay of Vila Formosa, a São Paulo cemetery, digging up graves to make room for the rising body count. But moving bones into ossuaries after a period in the ground is a common Portuguese reburial practice, and by no means the apocalyptic outcome it sounds like in English. Coronavirus is actually calming down a bit in Brazil, leading to the usual hand-wringing over the reopening of the Brazilian economy.

Of more interest are the Indonesian body snatchers liberating the dead for Islamic burial. The New Straits Times carefully omits the religion involved, while going into great detail about security forces' various failed attempts to enforce quick burials of those dying of COVID-19. The UCA (Catholic) News is clearer about the Moslem motivation for the body snatchings, but also mentions that there's already a fatwa against such burials.

Back in the land of the living, China's case count has jumped from their usual see-no-evil trickle of cases to a cluster of 53 cases in Beijing. A whopping 46 of the 53 are asymptomatic; most have been traced as far as a wholesale vegetable market but no further. PlagueBlog would call it your usual sign of cryptic community spread in a country going out of its way not to test anymore, but surely China will eventually find some foreign visitor to pin it all on.

Massachusetts cases are up a third of a percent again today.

Day 133: Attack of the Mutant Spike Protein

The New York Times reports on a preprint about a mutation (D614G) in the SARS-CoV-2 spike protein making it more stable, and therefore, possibly, more infectious. This spikier mutant coronavirus has become predominant over time, especially in Europe and the northeastern US, but was not present in earlier outbreaks in the northwestern US.

A press release at Scripps about the paper discusses some reasons why many researchers have picked up on the mutation itself without establishing whether it contributed to the virus's fitness or merely spread through founder effects. While they feel they've established increased infectivity of the mutant virus in the lab, they stop short of claiming that the result definitely holds under real world conditions.

Interestingly, the paper itself discusses the "natural" history of the furin-cleavage site (which PlagueBlog readers may recall also figures into unnatural histories of SARS-CoV-2) and how this previous change gave rise to the need for more stability in the spike protein that would have favored a mutation like the one under discussion. Their point stands regardless of how the furin-cleavage site made it into the virus.

Elsewhere on the research front, an Indian study of hydroxychloroquine as a prophylactic treatment has shown promising results. A comparative study of BCG, pneumonia, and flu vaccination found reduced mortality associated only with the BCG (tuberculosis) vaccine. Also, the asthma question has an answer in pre-proof: a study by the Harvard School of Public Health found that non-allergic asthma increased the risk of developing severe COVID-19, but that allergic asthma did not.

Some correspondence to the Lancet concludes against herd immunity based on very little evidence and some rather questionable assumptions ("probable similar previous exposure to other human coronaviruses", "lockdown would not alter the herd immunity threshold in the population or the ultimate death rate per capita"). Demographic differences between European countries were explicitly brushed off, and other differences (superspreading history, spikier viral mutations, etc.) were not even considered.

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

Day 132: Making it Worse

The world has accumulated 7.5 million coronavirus cases, with nearly 423,000 deaths. The US (over 2 million cases) is slowly creeping upwards at a rate of 20,000 cases or so a day. Second-place Brazil has topped 800,000 cases and 40,000 deaths. Russia (#3) has exceeded 500,000 cases, and today India jumped past both the UK and Spain to hit fourth place just shy of 300,000 cases. Massachusetts cases are up half a percent today.

The Wall Street Journal has put together a scathing overview of the state's delayed and counterproductive reaction to the coronavirus: How New York’s Coronavirus Response Made the Pandemic Worse. PlagueBlog did not find most of it all that damning; it's not clear that a few days' delay in closing schools and other "slow" reactions really made much of a difference compared to the CDC's only-ex-China testing policies (for which New York is also unfairly blamed):

In early March at Health + Hospitals' Elmhurst, Dr. Chad Meyers and his colleagues in the emergency room worried they were missing community spread of Covid-19. But when they called the city’s health department to get patients tested, it rejected for testing even many patients who satisfied the criteria, Dr. Meyers said, leading to “often protracted and unproductive calls” with the department.

Hospital, city and state officials said they were relying on the federal government for testing capability and were limited by criteria set by the Centers for Disease Control and Prevention on whom they could test. Jason McDonald, a CDC spokesman, said: “CDC testing guidance has always allowed for clinical discretion. So, while we set guidelines, states and health-care providers have had the flexibility to determine who to test.”

I'd blame the CDC for that one, although it does sound suspiciously like Governor Cuomo's argument that the nursing homes never had to take the COVID-19 patients he forced on them.

The state's called for a 50% increase in beds with little provision for a corresponding increase in staffing, though to what extent that was a true "misstep" is unclear from the anecdotal nature of the evidence. Statistics of ventilator deaths from lack of training or substandard equipment should not be taken too much to heart, considering the generally low rate of survival of COVID-19 patients on ventilation.

The article becomes quite torn on the topic of equipment and oxygen shortages; the anecdotes say there weren't enough, and the administrators and spokespeople say there were no shortages. There's also a question of how healthy and well-documented the patients who were transferred between hospitals were. A spokeswoman blamed the generally unstable condition of COVID-19 patients for the nearly-dead-on-arrival transfer phenomenon.

Perhaps most damningly, there was a policy of neither testing nor furloughing exposed and/or asymptomatic staff, due in part to the shortage of tests (not to mention the shortage of staff). The most dangerous choice of all, however, merits only an aside in an anecdotal story about PPE: an executive committed suicide over PPE procurement "among other issues nursing homes faced," such as the flood of COVID-19 cases forced on them by the state.

Day 131: Not Fantastic

RTE reports that an Irish virus expert has made a bit of a splash about masks:

The Director of the UCD National Virus Reference Laboratory has told the Dáil's special Covid-19 committee that the evidence around the use of cloth masks is "not fantastic".

Dr Cillian De Gascun told the committee the uptake of masks had not been very large, but added that there was not great evidence that the virus was stopped by non-medical grade or cloth masks.

He said that while medical grade masks worked very well, inappropriate mask use could be potentially harmful and could increase the risk of transmission.

A brave Redditor produced a nice collection of references in reaction to the news, but another Redditor's more humorous response also deserves attention:

Covid Rule No. 1
You can go to a bar and have a drink.
But only if the bar sells food and you have food with your beer.
The only logical reason for this :
Food prevents the spread of C19
​
[...]​
​
​ Covid Rule No. 3
You can go to a hardware store but homeware stores are not allowed to open. However, if the hardware store also sells homeware, that store is allowed to open and you are allowed to purchase homeware from that store.
The only logical reason for this :
You can contract C19 from homeware, but the presence of hardware wards off C19 like crucfixes warn off vampires.

Doubtless due to our rigorous warding off of vampires, Massachusetts' cases are up only a quarter of a percent again today. It's also cities and towns day, and except for the usual tiny towns and a tad bit of activity in the Fall River area (up 8% over the week compared to the state average of 2%), things are looking very quiet:

(Pop out.)

Day 130: Retractions

Well, you know the moment the WHO says anything for the sake of science rather than China, it's going to get retracted, but they usually don't operate at the whiplash-inducing speed PlagueBlog has experienced in the last 24 hours. Axios reports that the WHO has already "walked back" yesterday's comments that asymptomatic spread is "very rare". Of course they can't call back the evidence that asymptomatic spread is very rare, but they can wring their hands about a lack of clarity in comments that were pretty clear about the difference between asymptomatic and pre-symptomatic spread, etc., etc.

Also on the retraction front, a couple of published papers and a preprint were retracted last week due to reliance on a proprietary data set from Surgisphere. The studies' conclusions included that ivermectin was effective against coronavirus, that hydroxychloroquine was dangerous to use on COVID-19 patients, and that ACE inhibitors were safe to use. This seems to be a bit of a tempest in a teapot; the issues of validating anonymized data are nowhere near the heart of the problems of peer review and reproducibility of science in normal times, never mind during a panic pandemic.

The saddest retraction of all, however, is the Commonwealth of Massachusetts' stealthy postponement of bar reopenings from Phase 3 to Phase 4, "which the administration has said will require a vaccine or effective treatment for COVID-19." Or in other words, until the lawsuit.

To be honest, there are not a lot of bars here that don't serve some kind of food (and thus probably still qualify for Phase 2 or 3), though it's unclear from the news reporting how much food service turns a bar from a forbidden nightclub back into a permitted restaurant. Cases are up a quarter of a percentage point in Massachusetts today, so I guess we need to suddenly panic about the occasional food-free bar.

Day 129: Aspreadomatic

The latest exciting semi-news out of the WHO is that asymptomatic cases of coronavirus do not contribute significantly to the spread of the disease. It's not really news in that the WHO noted back in April that not a single case of asymptomatic spread had been documented. But it does call into question wearing an ersatz mask that might protect others, on the off chance that you might cough or sneeze while you might be within six feet of another person, and you might be an asymptomatic carrier, and asymptomatic carriers might be infectious, and it might be possible to infect someone without having a prolonged conversation with them—even though none of those things are individually likely according to the science. They are even less likely in combination according to the math.

On the conspiracy front, PlagueBlog readers may recall some rumors of US intelligence about a disease circulating around Wuhan in the early fall. These reports have reentered the non-conspiracy news cycle on the heels of a paper appearing on at Dash, Harvard's preprint server. In Analysis of hospital traffic and search engine data in Wuhan China indicates early disease activity in the Fall of 2019, the authors analyzed both Baidu searches and satellite photos of the parking lots of hospitals in Wuhan from last fall, and discovered that the disease may go all the way back to August 2019:

In August, we identify a unique increase in searches for diarrhea which was neither seen in previous flu seasons or mirrored in the cough search data. While surprising, this finding lines up with the recent recognition that gastrointestinal (GI) symptoms are a unique feature of COVID- 19 disease and may be the chief complaint of a significant proportion of presenting patients. This symptom search increase is then followed by a rise in hospital parking lot traffic in October and November, as well as a rise in searches for cough. While we cannot conclude the reason for this increase, we hypothesize that broad community transmission may have led to more acute cases requiring medical attention, resulting in higher viral loads and worse symptoms. This temporal progression of clinical presentation from mild illness to more severe outcomes has been shown elsewhere.

Massachusetts cases are up 0.18% today. The Boston Globe has a running list of restaurants in eastern Massachusetts that have opened up with outdoor seating for Phase 2 where you can go out to celebrate our ever-dropping case counts. (Certain tin-pot-mayored cities are not featured on the list.)

Day 128: Stabbed in the Back by the Spike Protein

The world is at seven million cases with 406,000 deaths and about 3.5 million recovered. The US has reached two million cases with 112,000 deaths. While India has legitimately surpassed Italy to reach #6, it is still well in the lee of #4 Spain despite the usual rash of reports to the contrary. The UK, however, is looking to move up from #5 momentarily. Massachusetts cases are up 0.3% on the eve of Phase 2 of the state's reopening plan.

On the made-in-a-lab front, Forbes has published a Norwegian scientist's claims that SARS-CoV-2 was so made in a lab, and the Quarterly Review of Biophysics has accepted the article behind his claims, A Candidate Vaccine for Covid-19 (SARS-CoV-2) Developed from Analysis of its General Method of Action for Infectivity. Although the paper is nominally about their vaccine (Biovacc-19), the authors' approach relies upon their view of the virus as genetically engineered:

Although no other Covid-19 vaccine design programme appears to follow this methodology, we believe, from experience, that successful vaccine design logically starts with a thorough understanding of the aetiology of the target virus which appears in this case to be quite singular. In consequence of our researches and therefore unlike conventionally developed vaccines, Biovacc-19's Method of Operation is solely upon non human-like (NHL) epitopes which are 21.6% of the composition of this coronavirus's Spike protein.

Interestingly, their approach was honed not on the dark web of COVID conspiracy theories, but in the trenches of HIV vaccine development:

It is thirty six years since the world was promised an HIV vaccine that would be ready in eighteen months. We correctly predicted the failure of all three major HIV/AIDS vaccines over those years, and specifically the danger of poor immune responses to conserved human-like domains and antibody- enhanced infectivity to high mutating domains. Earlier this year, the latest South African trial was terminated due to futility in preventing HIV transmission (UNAIDS, 2020). From our past HIV experience, we therefore observe that in the present context, any vaccine design based on the whole Spike protein of SARS-CoV-2 may not be immunogenic due its high human similarity compared to a vaccine with specifically selected NHL epitopes, such as Biovacc-19 does - and is.

Covid-19 candidate vaccines designed without appreciating these problems may run similar risks to those experienced with HIV vaccines that failed to show protection. The possibility of inducing autoimmune responses or antibody-dependent enhancements, needs to be carefully guarded against because there is published evidence that an HIV candidate vaccine has actually enhanced infectivity (Duerr et al., 2012): "Vaccinations were halted; participants were unblinded. In post hoc analyses, more HIV infections occurred in vaccinees vs placebo recipients in men who had Ad5-neutralizing antibodies and/or were uncircumcised. Follow-up was extended to assess relative risk of HIV acquisition in vaccinees vs placebo recipients over time”. Such antibody-dependent enhancement (ADE) has been observed for coronaviruses in animal models, allowing them to enter cells expressing Fc𝛾R.

For specific accusations against the US and China for their gain-of-function viral research, you have to go back to the Forbes article. (This is left as an exercise for the reader.)

The PlagueBlog files contain another recent discussion of the stabby alien spike protein of SARS-CoV-19, the preprint The emergence of SARS-CoV-2 by an unusual genome reconstitution at Research Square. The authors found an unusual 7-amino-acid (7aa) sequence within the spike protein that they felt was unnatural, but instead of making accusations in Forbes they BLASTed it a lot until they found a matching sequence in Plasmodium malariae, the malaria parasite.

Crazier than made-in-a-lab though that may sound, the authors take it seriously. They conclude with some interesting speculation about using malaria drugs against COVID-19, and note yet another pattern distinguishing hard-hit Western countries with those places that are getting off easier: malaria prevalence.

Day 127: Neovisicide

PlagueBlog is saddened to have correctly predicted the planned slaughter of no-longer-particularly-sick mink (Neovison vison) in the Netherlands, due to their suspected ability to transmit coronavirus back to humans, as well as pure speculation that they may turn into an animal reserve for the virus (which hardly seems to need one with humans keeping it going). The Guardian reports that the unnecessary and paranoid gassing of mink mothers and their new pups has already begun. The Guardian misreports that the mink were initially infected by the farmers. In fact, the source of infection doesn't seem to have been humans; it may have been farm cats. (PlagueBlog hopes they won't also be gassed.)

Elsewhere on the animal front, the South China Morning Post reports that man's best friend can detect coronavirus infections. French researchers trained eight Belgian Malinois shepherd dogs to sniff out the infected from their armpit sweat. (No dogs were endangered in the course of this experiment.) They even found two asymptomatic cases in the control sweat samples; the corresponding humans were retested and found to be positive.

Cases are up only 0.56% in Massachusetts; to celebrate the governor is letting restaurants open for outside dining on Monday, though the state's tangle of pandemic web pages don't seem to include any confirmation of that yet.

Day 126: The WHO Dons Masks

Massachusetts cases are up half a percent today. Protests and riots continue, but one should not ask whether COVID-19 is over now.

The Guardian reports that, in a surprise move, the WHO has come out in favor of masks with a vengeance. Take that old Metallica t-shirt off your head, because the WHO recommends the sorts of masks no one has: "medical grade" masks for the elderly and ill. They taunt the rest of us with complex homemade masks the likes of which Pinterest has never seen:

All others should wear a three-layer fabric mask: absorbent cotton closest to the face, followed by a polypropylene layer and then a synthetic layer that is fluid-resistant, the WHO said. It envisages that these masks can be made at home, but that small companies may begin to produce them, also providing jobs.

PlagueBlog's experience of making masks at home is a bit different from the WHO's pipe dream. You can't even get elastics to go around your ears anymore, never mind unspecified fluid-resistant synthetics or polypropylene (which is not merely non-woven mask filter material, though that was already difficult to source). At least the WHO only recommends masks when you can't socially distance, unlike certain tin-pot mayors in the US.

On the breathable side, the Finnish government has rejected mask requirements out of hand. As you may recall, their health ministry came down against them last week, and the government has sided with them against another panel who reported in favor of masks.

Earlier this week, the New York Times reported on the inadequacy of surgical masks in a medical context. (Cloth masks were right out.) The paper behind the article is Physical distancing, face masks, and eye protection to prevent person-to-person transmission of SARS-CoV-2 and COVID-19: a systematic review and meta-analysis [PDF]. The PlagueBlog hopper also spit out a slightly older and more pessimistic paper on the topic of hospital protections: Universal Masking in Hospitals in the Covid-19 Era, which focuses on other precautions in hospitals, and tosses off this gem early on:

We know that wearing a mask outside health care facilities offers little, if any, protection from infection. Public health authorities define a significant exposure to Covid-19 as face-to-face contact within 6 feet with a patient with symptomatic Covid-19 that is sustained for at least a few minutes (and some say more than 10 minutes or even 30 minutes). The chance of catching Covid-19 from a passing interaction in a public space is therefore minimal. In many cases, the desire for widespread masking is a reflexive reaction to anxiety over the pandemic.

Day 125: In Your Genes

It came out in the autopsy that George Floyd was still positive for COVID-19 on a PCR test, after having previously tested positive on April 3rd. "It wasn't immediately clear whether Floyd developed symptoms earlier in the year or was an asymptomatic carrier," though the autopsy revealed no particular post-COVID-19 damage. It did reveal "hypertensive heart disease, fentanyl intoxication and recent methamphetamine use." As with the flu taboo, PlagueBlog is not supposed to mention the effects of fentanyl; we will have to leave that to the defendants' lawyers.

The New York Times seems to have misread a recent preprint on the genetics of coronavirus susceptibility as clearing ACE2 of involvement in severe cases of COVID-19 and only pegging blood type. But ACE2 is still a suspect; its colleague SIT1 is just mixed in with chemokine receptors at that locus, so the paper doesn't come down on either one as hard as on blood type. (If you haven't heard about the blood type correlation before, A is bad and O is good, possibly due to nearby genes as well.)

Here's the weekly map again, still without the new testing and positivity data. The upshot is much the same as in the past few weeks: mostly plateau, with some big-looking increases in small towns and some ongoing activity in Southeastern Massachusetts:

(Pop out.)

P.S. Massachusetts cases are up 0.46% today.

Day 124: A Snowball Effect

The stats are largely unchanged. Massachusetts cases are up 0.42% today, and there is both good and bad news about cities and towns day: it seems that the CDC's desire for probably cases has not yet affected the cities and towns data, but on the other hand, the MDPH's penchant for rearranging the data has mixed things up again. So any pretty pictures will be delayed until tomorrow.

On the mink front, coronavirus has been found at three more mink farms in the Netherlands, through mandatory mink testing. The report fails to mention whether the minks' contacts have been traced. It seems that coronavirus paranoia may lead to culling of the unfortunate and mostly recovered mink.

The US has a new first canine case, since the previous pug case was later retracted. The new patient is a German shepherd from New York State whose owners tested positive and showed symptoms, respectively. The dog showed respiratory symptoms, but is expected to recover. A second dog in the same household had antibodies.

An anti-vaxxer has tackled the far simpler challenge of debunking the "lockdown lunacy" at his blog. It's a long read, partly because every time you think you've gotten to the most damning evidence against lockdowns and the like, he comes up with something even more damning. His citations will be familiar to anyone who follows corona-science—that is, you don't have to be a conspiracy theorist to have heard most of it before. PlagueBlog had not heard the quote from which today's title was taken, though:

It is what is known in science as positive feedback or a snowball effect. The government is afraid of its constituents. Therefore, it implements draconian measures. The constituents look at the draconian measures and become even more hysterical. They feed each other and the snowball becomes larger and larger until you reach irrational territory. This is nothing more than a flu epidemic if you care to look at the numbers and the data, but people who are in a state of anxiety are blind. (Yoram Lass)

There was also a new-to-us paper in there, a contact study for an asymptomatic Chinese patient in a healthcare setting who managed not to infect 455 contacts. The blogger does leap to a conclusion here (that asymptomatic carriers are never infectious), though this patient may merely have been past the period of infectivity or otherwise atypical.

Day 123: Made in a Lab

In a fortunate moment of insomnia, one of PlagueBlog's vast team of reporters spotted a 338-page preprint on Reddit about how SARS-CoV-2 was engineered in a lab. The reporter was only a few pages into this fascinating read when the moderators found it and scrubbed it from Reddit—but not from viXra.org, an unmoderated preprint server set up to avoid censorship at arXiv.org. The paper, by graduate student Murat Seyran, is titled Host Change -Tropism [sic] Pattern of Human Coronaviruses Suggesting the Engineered Nature of Severe Acute Respiratory Syndrome Coronavirus 2.

Most of the 338 pages are the supplementary materials, including some nice tables comparing various coronavirus sequences, plus 7 less approachable sets of sequence alignment results that don't really fit the page format. The text itself is quite readable at only 15 pages, and nicely summarizes the seven known human coronaviruses and the (ongoing) changes from their animal sources that make them infective in humans. It's worth a read just for that, even if you're uninterested in the question of whether SARS-CoV-2 was bioengineered.

So what is suspicious about SARS-CoV-2? One issue is a change that didn't happen that normally does during coronavirus adaptation to humans:

[The] N-terminal domain (NTD) of CoVs Spike (S) Protein contains a specific glycan-binding region as the first contact area with the new host. Specific glycan-binding immune receptors e.g. C-type lectins recognize NTD of S Protein of CoV and exterminate the virus before its adaptation. [...] Strikingly, SARS-CoV-2 does not have a single amino acid (aa.) alteration or deletion on its glycan-binding region NTD of its S Protein compares to its parent virus BatCoV RaTG13. The flat and unsunken surface of SARS-CoV-2 NTD S Protein conflicting with the general adaptation and survival pattern of all CoVs.

And that's only the first difference of three. The second is that a "template-switching" model of coronavirus replication restricts mutations to certain sites. ("CoVs pause their replication on certain domains and have recombinations on these specific sites.") However, the second major mutation of SARS-CoV-2 involving the virus' use of host cell furin protease is not at one of these sites, and that suspiciously altered site continues to stubbornly not mutate in the wild:

However, other betacoronavirus lineage B members and the clinical strains of SARS-CoV-2 do not have any alterations on S Protein S1/S2 suggesting SARS-CoV-2 obtained this trait with a one-time unique event.

The third suspicious trait is similar; coronaviruses generally continue to adapt to the host in certain positive selection sites, including the receptor binding domain (RBD).

However, despite millions of SARS-CoV-2 infections, RBD has not indicated a single high-frequency aa. substitution suggesting the too-perfect angiotensin-converting enzyme 2 (ACE2) binding that was gained with a one-time alteration. Unlike the RBDs of other CoVs, SARS-CoV-2 RBD is not a positive selection site.

Besides the purely biological arguments, the author has some other evidence to bring to bear for bioengineering. Firstly, engineering coronaviruses was all the rage before a US moratorium on such research, and, possibly, afterwards. Secondly, coronaviruses are postulated to spread to humans through bat and camel droppings polluting the water supply, but China's bat diversity is relatively low and its water supply relatively safe from such issues.

The author concludes with a series of rhetorical questions reflecting what has come before:

The engineered origin of the SARS-CoV-2 was mainly rejected (Andersen 2020) the question is how SARS-CoV-2 survived the immunity of pangolins or humans during the very first interaction with its flat easy-target sialic acid-binding domain? SARS-CoV-2 indicate the low frequency of mutations on its RBD and how the virus obtained such effective RBD compositions without destroyed by pangolin or human immunity due to its easy target sialic acid-binding domain? Why only the RBD had mutations meanwhile the rest of the genome was almost unaltered? Betacoronavirus lineage B CoVs including SARS-CoV S Protein does not have a pattern of recombination on S1/S2 region how SARS-CoV-2 obtained that ability and how we do not see any further recombinations in the clinic SARS-CoV-2 strains? SARS-CoV-2 clinic strains do not have any high-frequency mutations on NTD and RBD how the virus obtained such perfect and precise host cell membrane interaction capacity, unlike SARS-CoV, perished due to its failed adaptation? Why we have not seen any pandemic caused by CoVs before? Why these pandemics did not emerge in places where people rely on water sources shared with bats or bats consumed as bushmeat? In summary, if SARS-CoV-2 is not an engineered Bat CoVs RaTG13, its unnatural host tropism pattern and pandemic potential compare to other human pathogenic CoVs raising those questions.

It's interesting that the author is suspicious of SARS-CoV-2 despite accepting the bat coronavirus BatCoV RaTG13 as its natural ancestor, because other made-in-a-lab theories are equally, if not more, suspicious of RaTG13 itself.

If you follow the conspiracy theories, you have probably heard of "batwoman" Zhengli Shi, a researcher from the Wuhan Institute of Virology who allegedly discovered RatG13 in 2013, although the sequence was not published until this January as part of a COVID-19 paper and (so the conspiracy theory goes) the samples may not be extant, if they ever were. (The alternative hypothesis is that the sequence was invented as a missing link to conceal the engineered nature of SARS-CoV-2.) Instead, the postulated ancestors of SARS-CoV-2 are BatCoV ZC45 and BatCoV ZXC21, plus Zhengli Shi. The similarities are explained at both the link above and in the related blog post.

If you're interested in more mainstream reporting on viral origins, ArsTechnica investigates a two-species origin theory, in which a pangolin takes on the role of Zhengli Shi. The source paper is here, with plenty of analysis of BatCoVs RaTG13, ZC45 and ZXC21, plus some PanCoVs.

PlagueBlog does not endorse any particular origin theory for SARS-CoV-2.

P.S. Massachusetts cases are up 0.36% today (probable cases included).

On the tin-pot mayors vs. state and federal constitutions front, a New Hampshire resident is suing the city of Nashua in Hillsborough County Superior Court South over face mask requirements exceeding those of the state.

In the lawsuit, Fojo argues that the city has failed to explain why its health officials are not heeding the guidance of the World Health Organization.

"The ordinance’s justification that 'slowing the spread' of the coronavirus is somehow still a societal objective also ignores the fact that the entire state of New Hampshire has been wildly successful at 'flattening the curve' since it never came close to reaching the capacity of its health care system," the complaint states.

Day 122: Another Great Leap Forward

Today marks the beginning of meteorological summer in the northern hemisphere. The world is at 6.37 million cases, with 377,000 deaths. Saudi Arabia has passed the China mark, and Mexico has surpassed both China and Canada to take fourteenth place (after Chile with 105,000 cases). And defenestration is still a major coronavirus complication in Russia.

Massachusetts cases are up only 0.33% today by our normal accounting methods, but, due to advice from the CDC about counting "probable" cases, our total case count has make an unexpected leap to over 100,000 cases, and our death count a smaller leap to 7,035 victims. PlagueBlog expects a similar disturbance in the cities and towns data come Wednesday, which will probably leave nothing useful to map until things settle out next week. At least we'll always have the Financial Times' excess mortality data.

On the scofflaw front, the town of Swansea apparently held a special town meeting today, apparently with social distancing. PlagueBlog suspects that more than ten persons were in attendance, but PlagueBlog also doubts that the constitution of the commonwealth permits the governor to cancel town meeting for the flu.

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.