Day 151: The Zombie Uprising

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

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

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

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

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

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

Day 150: The Second Wave

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

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

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

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

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

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

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

Day 149: Hyperventilation

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

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

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

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

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

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

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

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

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

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

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

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

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

Day 148: The Unknown Knowns

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

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

PlagueBlog readers may recall this famous Donald Rumsfeld quote:

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

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

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

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

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

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

Day 147: Is it the Air-Conditioning?

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

Day 145: Houston, We Have a Problem

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

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

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

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

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

(Pop out.)

(Pop out.)

Day 144: The Real Surge

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

Day 143: Counterfeit Hand Sanitizer

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

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

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

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

Day 142: Nine Million Cases

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

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

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

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

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

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

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

Day 141: No Mask Day

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

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

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

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

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

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

Day 140: Rise of the Masks

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

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

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

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

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

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

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

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

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

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

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

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

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

Day 139: Fire in the Hole

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

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

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

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

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

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

(Pop out.)

Day 138: Brother, Can You Spare a Dime?

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

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

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

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

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

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

(Pop out.)

Day 137: The Salmon Panic

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

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

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

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

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

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

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

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.