Day 76: COVID In, COVID Out

Massachusetts' numbers are up 7.5% today. Yesterday the state promised some extra data (h/t MassLive), but of course it took some digging around the website to find it. The state's numbers for hospital infections [PDF] include Steward Health Care hospitals and also suspected cases, which is probably why they're so much higher than the numbers from the Globe the other day. Buried elsewhere, there's also a chart of bed occupancy and capacity [PDF] by "region", including the beds in alternate sites like Corey Hill the BCEC.

The new town-by-town data [DOCX] conveniently includes the rate scaled to 100,000 "residents". (The vast majority of cities in Massachusetts don't actually have 100,000 residents, never mind the towns.) There is a promise to update the town-by-town data weekly, but nothing about maintaining the hospital data.

An archive of the daily reports has also appeared. Finding them had previously required the Wayback Machine to discover their somewhat unpredictable and sometimes misspelled URLs. The archive also includes the previously missing DOCX for March 9th. (PlagueBlog has not yet checked the full archive against our own archives for changes.)

Here is a long-awaited pretty picture, of the town-by-town case rates (per 100,000) through April 14th:
Click to enlarge. The yellow hotspot near Boston is Chelsea. The top 10 cities ratewise are: Chelsea, Brockton, Randolph, Williamstown, Lawrence, Everett, Longmeadow, Braintree, Revere and Norwood, in that order. Holyoke is #11 and Littleton is #14, presumably due to their nursing home issues.

I made up the rates for the places with <5 but more than 0 cases; next time I will find population data for those places in order to estimate them properly (though it's unlikely to change the map much).

Day 75: Don't Be Alarmed

The world topped two million cases last night and now stands at 2,075,000, with 134,000 deaths. The standings are mostly unchanged, with the US at 641,000 cases and 28,000 deaths, and New York State now well ahead of Spain in cases (213,000 vs 177,000), though not deaths. Nevertheless, Dr. Fauci thinks we're finally flattening the curve.

ProPublica published a report on excess deaths in the US not yet attributed to coronavirus. It singled out Massachusetts and Detroit as particularly likely to be undercounting:

In Middlesex, Massachusetts’s most populous county and home to Cambridge, Somerville and Lowell, officials reported 317 at-home deaths in March. That’s about a 20% increase from the same time period for the past three years, in which deaths ranged from 249 to 265. [...]

Older people are particularly vulnerable to dying from COVID-19. In all of Massachusetts, deaths for people 65 and older increased by 3.6% in March from the same month, on average, during the previous three years. The comparison to 2019 was particularly dramatic, an additional 250 deaths across Massachusetts. At the same time, the data shows that increase can’t be accounted for by the official coronavirus tally alone: only 89 deaths statewide were attributed to the virus in March, according to state Health Department data.

Detroit had an increase of 110 "dead person observed" calls in early April. Other places are not necessarily doing any better; in many states vital records retrieval is difficult, slow, or entirely suspended, so the data is not available.

Massachusetts' numbers are up 6% today, with 151 new deaths. We are nearing 30,000 cases.

While early reports out of China indicated little risk to pregnant women, a couple of cases of death late in pregnancy hit the news today: a case study from Iran and an NHS nurse.

The coronavirus crisis seems to have led to many people discovering the Internet for the first time, at least judging from the amount of hand-wringing and alarm-sounding going on over "fake news" and "conspiracy theories". I don't mean Starving cannibal rats swarm deserted US streets amid Coronavirus lockdown. Some people might call that "fake news", but we already had yellow journalism. Giving it a new name only confuses the situation.

Instead I mean the sort of alarm expressed by a doctor on Medium about a non-doctor on Medium's hemoglobin theory. I came across the non-doctor's theory on reddit, where you can still find the archived link and other details, including the salient point that, despite sounding original, the non-doctor was summarizing existing research. Like other theories out there in preprint right now (several of which have been PlagueBlogged), it was interesting but not yet substantiated. There is always a pattern of people getting upset that someone dared suggest their particular misreading of a preprint because it's somehow vaguely dangerous or irresponsible to say something the original author usually didn't even say. (PlagueBlog is not suggesting that the Medium doctor is unique; he's just a well-written example not buried in a comments section.)

So, after a good deal of scare-quoting and gatekeeping, the alarmed doctor admits that the non-doctor's theory is clearly based at least in part on existing research (which the doctor also happens to find "seriously flawed"). His conclusion, far more unsubstantiated than any mistaken inference in the essay he's criticizing, is that somebody posting a scientific (if ultimately incorrect) theory on the internet "can genuinely put lives at risk". PlagueBlog eagerly awaits the mass graves and the death count websites devoted to victims of in silico speculation of this sort.

It's especially disappointing when an actual scientist can't abide by the process of science. It's not even a tiny bit surprising when the average journalist can't abide the average Joe. For example, Vox bemoans that 30% of Americans believe the coronavirus "conspiracy" theory that it originated in a lab, probably accidentally. Note that no conspiracy is involved; it's just a theory about the origins of the virus, as Vox reluctantly admits:

The belief that Covid-19 was created by humans stems from speculation by some scientists during the early days of the outbreak that the virus came from a laboratory.

Note that this theory has still not been disproven, though it may not be as fresh and appealing as it once was. There is no particular reason for Joe to change his mind about it, because it's still a free country no matter how alarmed you are. Vox thinks that Joe, being lower class, is in far more danger from coronavirus than the average alarmed middle class hand-wringer, but it's not his idea that the virus came from a lab that endangers him. If anything that would make him more cautious.

Vox also notes (referring to an older article and poll) that over 40% of Americans and even more Fox News viewers believed that the epidemic was being exaggerated. While it's clear how this opinion (finally!) could pose a danger to some people were it wrong, Vox hasn't actually established that it's wrong. Even PlagueBlog believes the pandemic is being exaggerated, because what else is left for the media to report about? Everything but coronavirus has been cancelled. This leads to a natural exaggeration of a disease that is, despite its rising death toll, still not the Spanish flu.

It is possible to hold an informed opinion that the economic toll of the cure is worse than the death toll of the disease (and various similar notions Vox might dismiss as "skepticism"). The easily alarmed may not like or agree with such opinions, but that doesn't make the alarmed opinion the truth and Joe's opinions a conspiracy.

Day 74: R0 and Rt

Today's numbers are edging ever closer to 2 million cases, hovering around 1,950,000 at the moment. A few numbers have leaked out of North Korea: four doctors and 180 soldiers have died of coronavirus. (These deaths are not included in the world total.)

The UK has joined Italy and New York City in hitting the news for its statistically suspicious death rate. Just by checking death certificates for mention of COVID-19, the Office for National Statistics picked up 15% more deaths than previously counted. A redditor noted even more of a death disparity in the ONS chart summary points:

The provisional number of deaths registered in England and Wales in the week ending 3 April 2020 (Week 14) was 16,387; this represents an increase of 5,246 deaths registered compared with the previous week (Week 13) and 6,082 more than the five-year average.

Of the deaths registered in Week 14, 3,475 mentioned “novel coronavirus (COVID-19)”, which was 21.2% of all deaths; this compares with 539 (4.8% of all deaths) in Week 13.

That's a difference of 2,607 unexpected deaths still not attributed to COVID-19. Unlike Italy and NYC, the health care system in England and Wales is not overwhelmed, so there's not a lot besides coronavirus to explain the extra deaths.

Circumstances have forced PlagueBlog to add the USS Theodore Rooosevelt to the germ boat list at #23, due to a death onboard from coronavirus. The unnamed sailor was found unresponsive last Thursday, two weeks after having tested positive, and died in intensive care on Monday. The case count aboard #23 is 585 positive out of a crew of 4,800. Rumor has it that four other infected sailors are in a hospital ashore; presumably the rest remain aboard.

Likewise, the USNS Mercy hospital ship has earned the title of Germ Boat #24 with its own outbreak. In this case they are combatting the outbreak not in the Diamond Princess way of Germ Boat #23, but by removing the seven infected sailors and their contacts to isolation ashore.

R₀, the basic reproduction number, is a somewhat vaguely defined measure of the number of people one infected person will infect in a naive population taking no precautions. For example, R₀ for measles, an extremely contagious and truly airborne disease, is generally estimated at 15. The CDC has estimated R₀ for coronavirus at 5.7 (revising an initial estimate of 2.45).

R₀ is contrasted with the effective reproduction number R (or R_t, or R_e), which is the average number of people infected by one infected person in the current situation (of precautions, partial herd immunity, etc.). Gabriel Goh at OpenAI has written a fun tool for playing with these values and others to see how they affect "the curve". Kevin Systrom, cofounder of Instagram, has a writeup about R_t as a useful, local metric of how individual US states are doing. He's pretty pessimistic about Massachusetts and Rhode Island:

Which states have the epidemic least “under control?” To answer this, I plotted states where the best case (eg. low end of HDI) is above 1.0, indicating the true value of Rt is almost certainly above 1.0. Surprisingly, Rhode Island, Maryland and Massachusetts sit at the top. Part of this may be that Rhode Island is earlier in its infection curve, but seeing large states like Massachusetts and Texas above 1.0 is worrisome—especially because none of these states have hit the headlines as being trouble spots.

P.S. Massachusetts' numbers are up 5% again today. Hospitalization numbers have dropped out of the report for undocumented reasons. (Speaking of which, the Boston Globe published a hospital-by-hospital breakdown of coronavirus cases, though Steward Health Care hospitals are omitted.) Middlesex holds a commanding lead over Suffolk County, and at least one Middlesex County mayor has decided to confuse matters by issuing hiss own mask guidelines in contradiction of the CDC and state guidelines.

Day 73: Super-Spreading

The world is at nearly 1,925,000 cases, with 119,000 deaths and 445,000 recovered. The standings haven't changed much, although Massachusetts (up only 5% today due in part to a change in reporting times) has moved up to third place in the US in a general scramble of the 20,000+ states. PlagueBlog wonders whether there is a strain difference going on, as our coronavirus strains are predominantly from the disaster area that is Europe, while the west coast, like Asia in general, seems to be doing far better with their direct-from-China strains.

A few other theories about the strange pattern of contagion involve super-spreaders. A preprint from March postulated compound super-spreading: Do superspreaders generate new superspreaders? a hypothesis to explain the propagation pattern of COVID-19, by Pablo M. Beldomenico in Argentina. He believes that a sort of cascade of super-spreading through high viral loads is what led to the heterogeneity of sudden outbreaks in places like Italy versus slow burns in places where you wouldn't expect them, like Japan. He brings in some evidence from experiments with veterinary diseases to bolster the high viral load part of the theory. He concludes thus:

If superspreaders generate new superspreaders by exposing susceptible people to large viral loads, this mechanism should be immediately acknowledged and considered in the responses being undertaken. In particular, emphasis should be placed on the isolation or strict distancing of people of risk groups, as they would not only have more chances of developing a more severe disease (with the potential of overwhelming the health system), but they could also be source of high viral loads.

The New York Times reports (some more) about the super-spreading event at Biogen, and the New Yorker reports on a super-skiing event in Idaho. (Viral loads are not documented.)

Let us not forget South Korea's infamous Patient 31. While there are other clusters in South Korea, hers takes the super-spreading cake. Back in the US, Channel News Asia reports on a man in Chicago who super-spread at a February funeral and a subsequent birthday party, infecting at least fifteen people and killing three. Note that the article suggests coronavirus could be more contagious than measles; it is not. Nothing is as contagious as measles, with an R₀ of about 15, and no one has suggested anything like that for COVID-19.

More on R₀ tomorrow...

Day 72: Coronascience

The numbers accelerate apace; most notably the UK has risen above the China mark to 84,000 cases and well over 10,000 deaths. (On the bright side, Boris Johnson is out of hospital.) In Massachusetts, we're up 2,615 cases (11%) to 25,475, with 70 new deaths. One notable death was of a whistleblower nurse at the Life Care Center of Nashoba Valley in Littleton, where ten residents have died and 67 have tested positive. (The surviving staff are still being tested.)

Non-pneumonia symptoms have been getting more attention lately. A 400% jump in at-home cardiac arrest deaths in New York City has been attributed to viral myocarditis or some other mechanism by which the virus is damaging the heart. JAMA Cardiology has a detailed case study of a healthy patient with cardiac complications. An autopsy study in New Orleans found cardiomegaly, right ventricular dilatation, and "scattered individual cell myocyte necrosis" in the heart muscle. (There's an interesting discussion of the autopsy results on reddit.)

Another non-pneumonia symptom that, like sudden cardiac arrest, may explain early rumors of people dropping dead in the streets is stroke. JAMA Neurology published a paper yesterday about neurological manifestations of coronavirus in patients in Wuhan. They noted that "[s]ome patients without typical symptoms (fever, cough, anorexia, and diarrhea) of COVID-19 came to the hospital with only neurologic manifestation as their presenting symptoms."

Seventy-eight patients (36.4% [of 214]) had nervous system manifestations: CNS (53 [24.8%]), PNS (19 [8.9%]), and skeletal muscle injury (23 [10.7%]). In patients with CNS manifestations, the most common reported symptoms were dizziness (36 [16.8%]) and headache (28 [13.1%]). In patients with PNS symptoms, the most common reported symptoms were taste impairment (12 [5.6%]) and smell impairment (11 [5.1%]).

Another new category of symptom to pop up is dermatological: a French medical society has published a press release claiming that rash unaccompanied by pulmonary symptoms may indicate asymptomatic COVID-19 infection.

On the reproduction front is a preprint out of England about anosmia as a predictor of infection. They used app data from Britain to "find that loss of smell and taste were present in 59% of COVID-19 positive individuals compared to 18% of those negative to the test [...] We also find that a combination of loss of smell and taste, fever, persistent cough, fatigue, diarrhoea, abdominal pain and loss of appetite is predictive of COVID-19 positive test with sensitivity 0.54, specificity 0.86".

On a different sort of reproduction front, South Korea reported a total of 91 relapses on Friday, up from 51 total on Monday. For some unknown reason, officials believe these cases are "reactivations" rather than reinfections, even though Korean patients must test negative twice before being counted as recovered.

There has been some progress combatting the cytokine storm with the CCR5 antagonist leronlimab. An Israeli treatment involving placental cell therapy and a stem cell therapy from Australia have also shown promise.

A drug target of interest is the bradykinin receptor type 1 (B1), according to a theory in preprint:

We propose it all starts with ACE2 and its role in the kallikrein-kinin system, which to date has not investigated in the pathogenesis of SARS or COVID-19. The kinin-kallikrein system is a zymogen system that after activation leads to the release of the nona-petide bradykin that after binding to the B2-receptor on endothelial cells leads to capillary leakage and thus angio-edema. The prototype diseases of local peripheral transient increased bradykinin release are hereditary or acquired angio-edema. The clinical picture of COVID-19 is in line with a single-organ failure of the lung that is due to edema at the site of inflammation.

In shorter words, the virus' use of ACE2 receptors on lung cells uses them up, causing them to fail at one of their important jobs: keeping fluid from leaking into the lungs.

P.S. PlagueBlog forgot to mention that John Conway died yesterday of coronavirus. He was 82 years old.

P.P.S. Another approach to the cytokine storm is cytokine blockers, as recently discussed in The Lancet.

Day 71: BCG vs RCV1

Today's numbers are impressive: over 1.75 million cases worldwide, with well over 100,000 deaths. The US (with over 500,000 cases) has finally pulled ahead of Italy and exceeded 20,000 deaths. The UK probably won't hold on to its 7th place below China for long but remains there now, and Boris Johnson is out of the ICU.

New York State (at 180,000 cases) remains ahead of the major European hotspots. New Jersey is a distant second at 58,000 cases, and the remaining hotspots (Michigan, Pennsylvania, California, Massachusetts, Louisiana, Florida, and Illinois) are all hovering around 20,000 cases. Michigan has locked down for real this time, forbidding travel between homes and "public or private gatherings of any size."

Massachusetts' numbers are down again today, with 1886 new cases (up 9%) and 87 deaths. The state is now tracking deaths in long-term care facilities (304 total) along with infections (2645, which includes health care workers) and infected facilities (190). Also of note, the sidewalks of one street in Beverly have been declared one-way.

With Wyoming jumping on the bandwagon, all 50 states (plus 4 territories and the District of Columbia) have declared disasters simultaneously for the first time.

So, why us? You've heard this explanation here before, but since the media has picked up on another paper (apparently the fifth) about the correlation between tuberculosis vaccination and low case fatality rates from coronavirus, you're about to hear it four more times.

The Bacillus Calmette–Guérin (BCG) vaccine uses a live, attenuated strain of Mycobacterium bovis (yes, it's a real vaccine, perhaps even more so than vaccina). It protects against tuberculosis (Mycobacterium tuberculosis) and leprosy (Mycobacterium leprae and M. lepromatosis) to some extent, for a couple of decades. It has long been known to protect against other respiratory diseases indefinitely, by a still unknown mechanism; it is also sometimes used in the treatment of bladder cancer. Nevertheless, adoption of BCG vaccine varies by country, perceived risk of TB, and time; see the BCG World Atlas for lots of details.

1. Back in the day, PlagueBlog covered the first preprint on this topic, Correlation between universal BCG vaccination policy and reduced morbidity and mortality for COVID-19: an epidemiological study, by Aaron Miller, Mac Josh Reandelar, Kimberly Fasciglione, Violeta Roumenova, Yan Li, and Gonzalo H. Otazu, at several New York institutions. They said:

We compared large number of countries BCG vaccination policies with the morbidity and mortality for COVID-19. We found that countries without universal policies of BCG vaccination (Italy, Nederland, USA) have been more severely affected compared to countries with universal and long-standing BCG policies. Countries that have a late start of universal BCG policy (Iran, 1984) had high mortality, consistent with the idea that BCG protects the vaccinated elderly population. We also found that BCG vaccination also reduced the number of reported COVID-19 cases in a country.

They controlled for income and also charted start years of BCG vs. deaths for countries that do or did vaccinate.

2. Another early paper, BCG vaccination may be protective against Covid-19 by Paul K. Hegarty, Ashish Kamat, Helen Zafirakis, and Andrew DiNardo (two Brits and two Texans) quantified both the infection and death rates over a fifteen day period in March at almost 10 times lower with BCG vaccination. They did note that "[c]ountries that have a booster injection of BCG 7 to 14 years later had no better outcomes than those with a single inoculation only."

3. The story currently in the news is about a preprint by researchers at Johns Hopkins that estimated a death rate only 6 times lower with BCG: Differential COVID-19-attributable mortality and BCG vaccine use in countries, by Anita Shet, Debashree Ray, Neelika Malavige, Mathuram Santosham, and Naor Bar-Zeev. The mortality rate is 5.8 times lower in vaccinated populations than in the unvaccinated. The average death rate per 1 million people in vaccinated countries is 0.6, while in unvaccinated countries it is 8.6. (If you're curious about country by country data, take a look at this supplemental figure.)

4. An even more recent paper, Mandated Bacillus Calmette-Guérin (BCG) vaccination predicts flattened curves for the spread of COVID-19 by Martha K. Berg, Qinggang Yu, Cristina E. Salvador, Irene Melani, and Shinobu Kitayama at the University of Michigan, compared infection and death rates in the first 30 days of a country's outbreak to their BCG status. Countries with vaccination policies that did not last into this century (e.g., Spain, Germany) turned out to be equivalent to those who never vaccinated (e.g., the US, Italy). In the supplemental material, they "predict" the numbers for an alternate US with full BCG vaccination:

This analysis applied to the number of cases yielded a predicted value of 11.28, which translates to 79488.86 cases (compared to the actual 213372 cases reported in the US by April 1). This analysis applied to the number of deaths yielded a predicted value of 4.54, which translates to 93.97 deaths (compared to the actual 2467 deaths reported in the US by March 29).

5. There seem to be more than five such papers, so I'm picking a fifth from among the related preprints at medRxiv that contradicts the others: Association Between BCG Policy is Significantly Confounded by Age and is Unlikely to Alter Infection or Mortality Rates by Stefan Kirov of Bristol Myers Squibb. The title says quite a bit, but the author also notes a confounding correlation between BMI and BCG policy: countries with lower BMI also have BCG vaccination. (Obesity is a known risk factor for coronavirus.) He attempts to make a spurious connection between rubella vaccination and (poor) COVID-19 outcomes as a sort of cautionary example, but rubella vaccination dates back to 1964 at the earliest (while BCG is over a hundred years old) and thus is much more confounded by age than BCG coverage could possibly be. Rubella is also a poor choice of counterexample because rubella vaccine (RCV1) coverage has been fairly consistent across the western world (except, notably, in Italy), where the contrasts in outcome despite few cultural and biological confounders led to such a baroque theory as BCG in the first place.

One preprint from yesterday goes full on in the rubella direction with a study of the MMR vaccine: Homologous protein domains in SARS-CoV-2 and measles, mumps and rubella viruses: preliminary evidence that MMR vaccine might provide protection against COVID-19 by Robin Franklin, Adam Young, Bjoern Neumann, Rocio Fernandez, Alexis Joannides, Amir Reyahi, and Yorgo Modis (mostly in Cambridge, England). Though they accept the BCG theory at face value and postulate that adoption of the MMR vaccine might follow a pattern similar to that of BCG, for this paper the confounding element of age for BCG is the primary explanatory factor. Age is strongly correlated with MMR coverage because MMR only dates back to the early 70's, and its constituent vaccines only date to the late 60's. Because rubella vaccine was also given to women of childbearing age, immunity to COVID-19 would be increased differentially for women over 50 vs. men of the same age. (Unfortunately the figures for this in the paper are mostly unlabelled and inscrutable.)

They also found similarities in the viral genomes of SARS-CoV-2 and the measles, mumps, and rubella viruses; there are quite a few details there, but no wet results yet. However, they have collected rubella immunoglobulin data in severe vs. mild cases of COVID-19:

A further prediction of our hypothesis is that there should be a specific rise in rubella Immunoglobulin G (IgG) titres in COVID-19 patients, and that these should correlate with disease burden as a marker of immunogenicity against SARS-CoV2 [...]

Patients with a high severity illness had on average increased levels of rubella IgG (161.9+147.6 IU/ml) compared to patients with a moderate severity of disease (74.5+57.7 IU/ml) (Fig. 5). In comparison, Immunoglobulin M (IgM) levels were 0.21+0.16 IU/ml in severe disease and 0.26+0.21 IU/ml in moderate disease. Whilst we accept that it is possible that this trend could be representative of preinfection protection to rubella infection, it is not possible to determine this. In a study of 160 women of child bearing age, the IgG levels of non-infected patients measured between 24-143 IU/ml, suggesting that it is unlikely that those who developed severe symptoms of the disease had IgG levels far in excess of this prior to infection.

Day 70 Retrospective: Even the Ya̧nomamö

PlagueBlog apologizes for being unavailable for day 70. (We are not infected.) Massachusetts was down in absolute case numbers, and went up by only 11%. Also the Governor signed a bill waiving the MCAS testing requirements this year. It's unclear whether MCAS high school graduation requirements (of having passed the tests) will also be waived. CNN reports that the feds are also investigating the Holyoke Soldier's Home:

According to the state's Executive Office of Health and Human Services (EOHHS), which runs the facility, as of April 9, 69 residents and 68 staff had tested positive for coronavirus. Since March, 32 residents of the home have died with 28 of those testing positive for Covid-19.

On Friday, April 10th, Reuters reported that a fifteen-year-old Ya̧nomamö boy from Rehebe named Alvanei Xirixan died of coronavirus in a hospital in Boa Vista, Roraima, Brazil. (The Yąnomamö are an indigenous tribe in the north of Brazil.) Some attempt to isolate other infected villagers is underway. Reuters also reported four infections among the Kokama tribe.

Day 69 Retrospective: Making the Diamond Princess Look Good

PlagueBlog apologizes for being unavailable for day 69. (We are not infected.) Massachusetts numbers were up 13%. Also, someone's been testing our sewage and thinks we have 100,000 cases, not 18,941.

The Germ Boat of the Day on Thursday, April 9th was #22, the Aurora Expeditions ship Greg Mortimer, on a 21-day Antarctic cruise out of Ushuaia since March 15th. Though its original destination was Puerto Williams, Chile, both Chile and Argentina have closed their ports, so the plague ship instead anchored in the Rio de la Plata (between Argentina and Uruguay) on March 27th, hoping to eventually dock in Uruguay. The Uruguayan government, for its part, refused docking until all passengers died tested negative. Note that 128 passengers and crew out of 217 are infected, including the ship's doctor, but Uruguay is keeping their social distance from all 217.

A week ago Saturday six especially ill passengers were evacuated in a PPE-heavy Uruguayan naval operation. Two more such passengers were evacuated on Wednesday. This Saturday the ship finally docked in Montevideo, where about 110 Australian and New Zealander passengers were escorted "along a 'sanitary corridor'" to a waiting charter plane.

The crew of 80, along with 20 European and American passengers, remain aboard the ship waiting to die test negative.

Day 68: Death Panels

PlagueBlog believes Massachusetts' numbers are to pattern, but has been distracted by the governor's announcement at his presser today that we're taking some advice from Pennsylvania about allocating scarce resources. As our peak is still predicted to exceed capacity, PlagueBlog is duly alarmed.

P.S. The numbers were up 10%.

Day 67: 5G

Today the world hit 1,430,000 cases with 82,000 deaths and 301,000 recovered. The US hit 400,000 cases and is quickly approaching 13,000 deaths. Spain, nominally #2 at 141,000 cases, is now actually behind New York State (142,000 cases), though Spain continues to exceed in deaths. France has not only passed the 100,000 mark but has leapfrogged over Germany to fourth place. Iran is sixth and the UK seventh with 55,000 cases, among them Boris Johnson, spending his second night in the ICU.

Massachusetts' numbers were a bit late today (though not as late as this post): 1365 new cases (up 10%) for a total of 15202, with 96 new deaths. The excess deaths have something to do with reports over the weekend not being correlated with cases until now. Suffolk has leapt ahead of Middlesex County again. There are now 958 positives at long-term facilities, and 129 facilities reporting COVID-19 cases. We almost hit 5,000 tests today. The governor talked about his testing goals at his presser today, but didn't explain the cause of the fluctuations.

PlagueBlog has heard some third-hand rumors that 5G causes coronavirus. They somehow predate Representative Mark Green's allegations yesterday that China was making the delivery of medical supplies to France contingent upon their using Huawei to implement 5G.

P.S. Gothamist reports an unusual number of deaths at home in New York City, which are not being reported in the official counts when they are untested, presumptive cases:

The FDNY says it responded to 2,192 cases of deaths at home between March 20th and April 5th, or about 130 a day, an almost 400 percent increase from the same time period last year. (In 2019, there were just 453 cardiac arrest calls where a patient died, according to the FDNY.)

That number has been steadily increasing since March 30th, with 241 New Yorkers dying at home Sunday — more than the number of confirmed COVID-19 deaths that occurred citywide that day. On Monday night, the city reported 266 new deaths, suggesting the possibility of a 40% undercount of coronavirus-related deaths.

P.P.S. On the bright side, Hong Kong pandas Ying Ying and Le Le used their newfound privacy to make more pandas.

Day 66: Opportunities for Fresh Disasters

Boris Johnson, who seems to be on oxygen in hospital at the moment, is a spicier G. K. Chesterton so far as quotability goes:

My friends, as I have discovered myself, there are no disasters, only opportunities. And, indeed, opportunities for fresh disasters.

The world has some large number of cases that have exceeded PlagueBlog's buffer. Spain, still a strong second place to the US, is contemplating universal basic income as a response to the pandemic. Germany has crossed the 100,000 case barrier, putting it in fourth place among nations. New York State is at 123,000 cases, over a third of all 337,000 cases in the US, and looks likely to overtake third-place Italy (129,000) soon. (IHME updated its projections for the US yesterday, including state-by-state peaks.)

The Feds, in their endearing way, confiscated a shipment of 35,000 N95 masks destined for Somerset County, NJ. One, it hardly seems worth it, and two, let's hope this drives home the lesson of how important it is to field your own successful football team for end-runs around the federal government.

On the cancellation front, Tomorrowland, an electronic music festival scheduled to be held in Belgium this summer, is on the chopping block. Also Gamestop got their plastic-bag-covered hands slapped last week for operating a non-essential curbside pickup business in Boston. Hopefully they've really closed this time and won't just pop up again like a bad mall kiosk.

P.S. The Guardian reports that Boris Johnson has been moved to intensive care.

Massachusetts' testing numbers are down again today from Saturday's high of almost 6,000 tests. Today only 4,500 or so were tested, with 1337 new cases (up 11%) for a total of 13837. (Middlesex County is back in the lead.) There were 29 new deaths. Once again, it was a lack of Quest test results that kept the numbers down. PlagueBlog suspects the feds are confiscating our swab supplies now.

Day 65: Summer is Cancelled

Today's Massachusetts numbers are suspiciously good: up only 764 new cases (7%) to 12500, with 15 new deaths. Upon closer examination, though, the drop seems to be due to a drop in tests completed (3137) to barely half of yesterday's 5838. The major Sunday vacationer was our major test provider, Quest, which completed under 1,000 tests today after having done over 3,000 on Saturday. So don't get your hopes up.

PlagueBlog is sad to report the first local cancellation of summer. Pinewoods Camp, Inc. has announced that it will remain closed all summer due in part to the difficulty of timing an opening for the camp in the current situation.

On the cat front, a tiger at the Bronx Zoo has tested positive for coronavirus, apparently due to exposure to an asymptomatic handler.

Zoo officials said Nadia, three other tigers, and three African lions have developed a dry cough, but are all expected to recover.

"Though they have experienced some decrease in appetite, the cats at the Bronx Zoo are otherwise doing well under veterinary care and are bright, alert, and interactive with their keepers," the zoo's release said.

Day 64: Black Cats

Today in Massachusetts we had 1334 new cases (13% over yesterday), and 24 new deaths. The US has more that 311,000 total cases, and Spain has surpassed Italy to earn second place. (This is especially impressive because Spain has only three-quarters the population of Italy.) Worldwide the total is over 1,200,000 cases and 64,000 deaths.

PlagueBlog has been remiss in report on pet infections. A Belgian housecat was confirmed to be the first feline patient on March 27th. "A week after its owner, the animal presented symptoms such as diarrhea, vomiting, and difficulty in breathing." A second feline case was found Monday, March 30th in an asymptomatic domestic short-haired cat from Aberdeen, Hong Kong, sent to quarantine when its owner fell ill and tested there.

At first the only cat concern was for the poor animals catching the disease from overly affectionate humans, but a preprint by Hualan Chen reports that both cats and ferrets can spread the disease, and cats can do so with "respiratory droplets." In another preprint, Chinese scientists tested stray and domestic cats in Wuhan, and found antibodies to SARS-CoV-2 in 15% of the hundred or so animals tested after the outbreak.

On the plague ship front, the title of Germ Boat #21 goes to the Coral Princess, which managed to accumulate two dead passengers on its way into the Port of Miami today. Not unlike Germ Boat #18, the Coral Princess thought it could get away with a cruise to South America a month ago, but cut the junket short in mid-March and started searching for any old port in a storm. They managed to dock in Buenos Aires for a day to offload some lucky passengers, but they turned into a germ pumpkin at midnight on March 19th and had to set sail again, this time for Fort Lauderdale. They finally docked in Miami this morning and offloaded the sickest passengers. An unfortunate passenger delayed sickening until later this afternoon, at which time his family got the run-around for hours until they called 911.

P.S. PlagueBlog is saddened to report that the death toll from methanol poisoning in Iran has reached 300 (or, by some reports, 480), and the injured exceed 1,000 (or possibly 2,850), due to the false belief that alcohol is a cure for coronavirus, along with a fatal lack of education about potable vs. poisonous alcohols. Deep distrust in their government that initially downplayed the virus may also be a factor.

Day 63: A Tale of a Fateful Trip

NHK News reports the current numbers in Japan, which include three previously unaccounted-for deaths for Germ Boat #2, the Diamond Princess, for an official total of eleven. PlagueBlog is aware of one Australian (James Kwan of Perth, 78) who tested positive after returning home and died there; he has never been included in Japan's official plague ship death toll. Wikipedia, however, has sourced the other deaths: Two Japanese men in their 70's died on March 22nd, and one Hong Kong woman in her 60's died on March 28th.

PlagueBlog is long overdue for a full accounting of who's been cruising for a COVIDding. Lists of the plague ships have appeared in Business Insider, NTD and the Telegraph (unpaywalled version). Business Insider's list is the most complete, but Wikipedia's list is by far the best documented and ordered. (Note that multiple sailings of the same plague ship are listed separately, and there are also more boats at Wikipedia than in their main list.)

GB #	Ship	WI #	BI #	Confirmed
1	World Dream	2		Yes
2	Diamond Princess	1	1	Yes
3	Anthem of the Seas			No
4	MS Westerdam	3	8	No
5	AIDAvita			No
	Voyager of the Seas	5, 10	30	Yes (previous trips)
6	Grand Princess	6	2	Yes
7	Carnival Panorama			No
8	Regal Princess		3	No
9	Costa Fortuna		7	No
10	Caribbean Princess		5	No
11	MS River Anuket/A'sara	4	10	Yes
12	RV Bassac Pandaw			Yes
	Ovation of the Seas	11	28	Yes
13	Ruby Princess	13	22	Yes
14	Costa Luminosa	12	17	Yes
15	Silver Shadow	7	12	Yes
16	Silver Explorer	8	13	Yes
	MS Braemar	9	11	Yes
	Celebrity Solstice	14	27	Yes
	Costa Magica	15		Yes
	Costa Favolosa	16		No
	Costa Victoria	17		No
17	Azamara Pursuit		19	No
18	MS Zaandam	18	29	Yes
19	MS Rotterdam			No
20	MV Artania	19		Yes
(21)	Coral Princess	?		Yes
	MSC Meraviglia		4	Yes (previous trip)
	Royal Princess		6	No (never sailed)
	MSC Opera		9	Yes (previous trip)
	Golden Princess		14	No
	Norwegian Jewel		15	No
	Pacific Princess		16	No
	Celebrity Eclipse		18	No
	Carnival Fascination		20	No
	Freedom of the Seas		21	No
	Azamara Quest		23	Yes (debated)
	Majesty of the Seas		24	Possible
	Norwegian Bliss		25	Yes
	Celebrity Summit		26	No
	MS Maasdam		31	No
	Carnival Valor		32	Yes (previous trip)
(22)	Greg Mortimer			Yes
(23)	USS Theodore Roosevelt			Yes
(24)	USNS Mercy			Yes
(25)	Charles de Gaulle			Yes
(26)	Oasis of the Seas			Yes
(27)	Symphony of the Seas			Yes
(28)	Norwegian Gem			Yes (crew)
(29)	Celebrity Apex			Yes (crew)
(30)	MS Roald Amundsen			Yes
(31)	m/s Paul Gauguin			Yes (crew)
(32)	SeaDream I			Yes (previous trip)
(33)	Etchizen Maru			Yes (fishermen)
(34)	HMS Queen Elizabeth			Yes

(Germ Boat numbers in parentheses were assigned after this post went up.)

As you can see, there were a lot of promising candidates, but the title of Germ Boat #20 goes to the freshest face on Wikipedia's list, the MV Artania, flying a Bahaman flag and currently anchored off Western Australia. After offloading most passengers, all Aussies, and all known coronavirus patients in Perth last month, the remaining 16 passengers (including 12 who were too sick or frail to fly home from Perth) and the crew seem fated to sail all the way home. They have not set sail yet.

P.S. Massachusetts' numbers are in. We are up 1436 cases (16%), for a total of 10402 with 38 new deaths (192 total). Cases in long-term care facilities are up 94% over yesterday to 382, possibly due to the completion of testing at the Holyoke Soldiers' Home, for which the Governor reported 51 positives 160 negatives at his presser today. (Speaking of the presser, someone may have made Rupert the sign language interpreter a fan subreddit today.) After having lagged behind the city for several days, Middlesex County has pulled ahead of Suffolk with 2202 cases vs. 2183, and Essex has firmed up its lead over Norfolk County.

PlagueBlog cannot overlook the irony that, due to cerveza being declared a non-essential industry in Mexico, Grupo Modelo has shut down production of Corona beer.

Day 62: Friends in High Places

The Wall Street Journal reports (sans paywall here) that 1.2 million N95 masks are on their way from Shenzhen to Massachusetts aboard the Patriots' 767.

Massachusetts’ quest to acquire these masks was a tense, weeks long saga that began with the state’s governor and winded through embassies, private partners and the U.S.’s most successful football franchise. After a layover in Alaska and an anxious process to win approval from Chinese officials, the plane was given permission to land in China to collect the masks.

“I’ve never seen so much red tape in so many ways and obstacles that we had to overcome,” said Robert Kraft, the Patriots’ owner.

The article notes that 300,000 of the masks will be sent on to New York, and half a million are still in China waiting for transport "on another shipment."

The Governor also spoke about it at his press conference this afternoon, referring to a previous shipment of 3 million masks that the state had bought from BJ's but that the feds confiscated in the Port of New York back on March 18th. The Boston Globe reported last week on that and several smaller incidents.

Bloomberg reports on our record unemployment, 6.65 million last week for a total of about 10 million in the past two weeks. They're hedgily predicting 15% unemployment in April and a possibly high of 20% if staying-at-home goes on longer than that.

P.S. The Governor also mentioned we will be giving an unspecified number of masks to Rhode Island as well. It's still open season down there, so PlagueBlog recommends not shooting the delivery folk if you want your masks.

P.P.S. The world has surpassed a million cases of coronavirus, with over 52,000 deaths. In Massachusetts, we went up 1,228 cases (16%) to nearly 9,000 cases. There were 32 deaths added, with one of a woman in her 30's in Suffolk County who had pre-existing conditions, but most over 60. Dukes (5 cases) and Nantucket (7) counties have finally been broken out. The state is also reporting some numbers regarding long-term healthcare facilities, where there are 197 individual cases and 85 different facilities reporting infections.

The Governor also mentioned at the presser that we're getting a Battelle N95 mask sterilizing setup at the empty K-Mart in Somerville, which should be sterilizing 80,000 masks a day by next week.

PlagueBlog neglected to mention that a 44-year old crazy man tried to ram a Navy hospital ship with a train in the Port of Los Angeles yesterday. PlagueBlog notes that psychosis is not a common symptom of COVID-19.

Day 61: April Fools

The civet saw its shadow, so we're expecting six more weeks of quarantine. Or something like that.

PlagueBlog is saddened to report the death of Star Wars actor Andrew Jack from coronavirus, and hopes he was able to leave a Do-Not-CGI order behind.

The world has exceeded 911,000 cases, and the US has surpassed the 200k mark and is already at 205,000 cases with 4,500 deaths. Italy is at 110,000 with 13,000 deaths, and Spain at 100,000 with 9,000 deaths. New York State is at 83,000 cases with 1,900 deaths, with New Jersey the runner-up at 22,000 cases but only 355 deaths.

There's an interesting preprint at medRxiv correlating the varying rates of COVID-19 morbidity and mortality across countries with their rates of tuberculosis vaccination:

BCG vaccination has been reported to offer broad protection to respiratory infections. We compared large number of countries BCG vaccination policies with the morbidity and mortality for COVID-19. We found that countries without universal policies of BCG vaccination (Italy, Nederland, USA) have been more severely affected compared to countries with universal and long-standing BCG policies. Countries that have a late start of universal BCG policy (Iran, 1984) had high mortality, consistent with the idea that BCG protects the vaccinated elderly population. We also found that BCG vaccination also reduced the number of reported COVID-19 cases in a country.

You can check out your country's BCG vaccination policy at the BCG World Atlas. Most notably, Spain had a child vaccination program from 1965 to 1981 only, though it appears that Basque children may still be getting vaccinated.

The Bozeman Daily Chronicle reports an undue touristic interest in Montana. The governor has expressed legal qualms about closing the border, trusting in the usual quarantine period instead. PlagueBlog recommends applying the National Guard to the issue instead.

The AP reports that Wisconsin is calling out the National Guard to staff polling sites for their primary next week, even though even Bernie recommends postponing the primary. PlagueBlog also recommends they save the Guard for a real election.

CNN Philippines reports that Duterte has declared open season on quarantine protestors. PlagueBlog is surprised it took him this long.

Time expresses the usual doubts about China's numbers, though in slightly different language than the usual urn-focussed story. Instead, Time opens with China's moving case counting standards:

After several days of trumpeting just a handful of new COVID-19 cases, on Wednesday China once again switched up exactly what that means, and included asymptomatic infections of the coronavirus in its official statistics for the first time.[...]

It was the eighth different definition of what constitutes a COVID-19 infection in China’s official statistics since the outbreak began in late December, with critics arguing that the lack of clarity has made it harder for other nations to adequately understand and prepare for the disease.

P.S. Our numbers are in: Massachusetts is up 1,118 cases (17%) to 7,738, with 33 additional deaths (122 overall). The state conducted a hundred-odd tests while Quest did 2,300 or so. Over 50,000 people have been tested; about 15% were positive.

The governor has also launched an independent investigation of the situation at Holyoke Soldiers' Home.

P.P.S. WFSB Hartford reports that a six-week-old baby has died of coronavirus there.

P.P.P.S. Something I didn't notice in our numbers at first was the death of 31-year-old Riley Rumrill of Suffolk County, an former Alabaman with pre-existing conditions (apparently asthma and obesity), and our youngest victim to date.

P.P.P.P.S. Also, there seems to be another Holyoke Soldiers' Home-level outbreak of stupid going on at the Life Care Center of Nashoba Valley in Littleton, MA. The town felt the need to publicize the facility's bad behavior in a press release.

Day 60: Even the Queen

PlagueBlog is saddened to report the death of the Spanish Royal Princess Maria Teresa de Borbón-Parma, aged 86. Having started on FaceBook, the news took some time to reach us.

USA Today reported yesterday that the Federal Reserve Bank of St. Louis is projecting an unemployment rate of 32.1% for the second quarter. Bodies are piling up at morgues in Iraq due to fears about burying them. Japan is planning to extend its entry ban to countries including China, South Korea, the US, the UK, and most of Europe.

On the mask front, CNN reports that the WHO has dug in in their recommendation against masks. People don't seem to be listening, though; more of the unqualified masses in the streets (and more specifically, the supermarkets) seem to wearing them every day.

Rhode Island was apparently not the first spicy island state to declare open season on tourists. El Pais reports that police in the Andaman and Nicobar Islands, an Indian territory, ejected at least thirty foreign tourists at gunpoint earlier this month, shipping them all to the airport on the main island where they were forced to buy plane tickets to the mainland (while being sprayed with window cleaner). The tourists now appear to be holed up in an abandoned embassy building in Chennai, because the locals there beat one of them up when he emerged.

The New York Times reports on a super-spreading event in Georgia similar to our ill-thought-out Biogen conference. Reuters reports on a super-spreading event in France that puts all of ours to shame:

The prayer meeting kicked off the biggest cluster of COVID-19 in France - one of northern Europe’s hardest-hit countries - to date, local government said. Around 2,500 confirmed cases have been linked to it. Worshippers at the church have unwittingly taken the disease caused by the virus home to the West African state of Burkina Faso, to the Mediterranean island of Corsica, to Guyana in Latin America, to Switzerland, to a French nuclear power plant, and into the workshops of one of Europe’s biggest automakers.

And last but never least, the plague ships: Tasmania's second death is directly linked to Germ Boat #13, the Ruby Princess. According to The Guardian, the ill-fated (and ill-docked) cruise ship transported 440 cases to Sydney, which represents 10% of Australia's total case count, and 5 of its 19 deaths.

In a move the NSW health minister later admitted was a mistake, 2,700 passengers were allowed to disembark without checks from NSW Health on 19 March, with many boarding flights interstate. Another boatload of passengers did the same on 8 March.

Since we're on the topic, DutchNews reports a Dutch national was the fourth to die aboard Germ Boat #18, the MS Zaandam (Holland America), which has been at sea for a two-week tour out of Buenos Aires since March 7th. Eight people have tested positive but about 200 are showing symptoms. After the Zaandam was refused docking at its original destination in Chile as well as in other South American nations, it spent some time anchored off Panama, where it transferred some healthy passengers to Germ Boat #19, the MS Rotterdam (so designated because, despite being apparently uninfected, it is as much of a pariah as #18 and is now also its travelling companion).

Panama reversed its initial decision and let both ships through the canal "for humanitarian reasons" on Sunday. The plague ships are now chugging towards Florida, though the governor has expressed his disinterest in allowing foreigners to be "dumped" in his state.

P.S. The Hill reports that the CDC may buck the WHO and encourage Americans to wear masks.

P.P.S. Today's Massachusetts numbers are up 868 (15%) to 6620. There were 33 more deaths, though, for a total of 89. Deaths are now broken out by decade (only one was under 60), county, hospitalization status, and pre-existing conditions (yes or no). Quest performed another 2,200 tests while the state did 20 (and also somehow went down one positive over yesterday). Suffolk County has pulled ahead of Middlesex again.

It's unclear how many of today's seven deaths in Hampden County are due to the "stunning breakdown of public health protocol" at the Holyoke Soldiers Home; the Boston Globe reports a death count of 13 with 17 cases among living residents and staff and more tests pending.

[Health and Human Services Secretary Mary Lou] Sudders said state officials are still trying to confirm important details, including precisely when the residents died, when they were tested for COVID-19, and who in their families were informed. She said the deaths were not reported to state officials.

Day 59: Mask Madness

Bolsonaro continues to keep Brazil open for business, saying "We're all going to die one day." (Todos nós vamos morrer um dia.)

Business is a little different in the Czech Republic, where Aktuálně.cz reports that 680,000 masks and 28,000 respirators were seized by the government after a local company attempted to sell them to the Ministry of Health at inflated prices. The reseller obtained the masks from one Zhou Lingjian, a man allegedly "directly linked" to the government of Communist China. All PPE was seized from his warehouse, including (allegedly) some intended as humanitarian aid for Italy. How the supplies stopped in Czechia instead remains unexplained, as the border was open for such shipments the whole time. The Czech police suspect theft.

Austria will be requiring people to wear masks in grocery stores starting Wednesday (free at the door), and recommends wearing them elsewhere. The FDA has approved using an Ohio company's mask sterilization technology at full capacity (80,000 masks a day), apparently in response to the governor's criticism of their initial arbitrary restriction to 10,000 a day.

The US has reached 164,000 cases, and Italy is now over 101,000. New York at 67,000 cases is ahead of Germany (66,000). Massachusetts has sadly risen in the rankings lately and is now at 5th in the nation with 5,752 cases (up 797 or 16% from yesterday). Eight new deaths, including several of people in their 60's, brings us up to 56 deaths.

Reddit reports that your Android phone will now warn you when you cross the state line into RI, where it's still tourist hunting season. PlagueBlog recommends turning off this feature if you live on the state line.

Day 58: Ash Lines and Riots

Today's numbers are down; Sunday seems to be the state lab's day of rest, and we'll surely get another Monday leap. Massachusetts now has 4955 cases, up 698 (16%) from yesterday, with 4 new deaths (all of persons over 70). Middlesex has retaken the lead with 981 cases as opposed to Suffolk County's 940. Essex has pulled ahead of Norfolk, 570–548. Quest tested 2,000 more people, while the state lab tested 2.

In Maryland, a man was arrested for inadequate social distancing outdoors. People seem to be smuggling video out of New York hospitals to the New York Times. If you want to know when your state will reach Peak New York, the Institute for Health Metrics and Evaluation at the University of Washington has projections for peak hospital demand (including how many hospital and ICU beds your state actually has). Just select your state from the dropdown to read 'em and weep.

There's also a new kid on the case-counting block, covidly.com, which makes nice graphs but doesn't seem to be updating in real time. Over on worldometers, the pandemic has already hit 718,000 cases with well over 33,000 deaths. Italy is nearing 100,000 cases. Spain is close to pulling ahead of China in cases, and is second only to Italy in deaths, if you believe China's numbers.

PlagueBlog's faith in China's numbers, if it existed at all, would be shaken from news out of Wuhan of thousands of people queueing up at funeral homes for urns of their relative's ashes. Urn counts have been estimated at 45,000, far in excess of the nation's official death toll of 3,300. Pictures and video of the ash lines posted to social media have been censored.

The Sun also reported rioting when residents of Hubei discovered their quarantine wasn't as over as they thought it was: they're still not allowed to travel around China.

P.S. After Cuomo threatened to sue, Rhode Island extended tourist hunting season to all out-of-staters. Those Massachusetts folks with houses straddling the state line should exercise caution when entering their living rooms.

Day 57: Turkey Sightings

With the world at 663,000 cases and 30,000 deaths, the US is firming up our grip on the lead with over 123,000 cases and over 2,000 deaths. Only Italy has also surpassed China, with 92,000 cases and 10,000 deaths (despite undercounting their deaths).

Today's count for Massachusetts is 4257, up 1017 (31%) from yesterday. In a surprise upset, Suffolk County has surged ahead of Middlesex County by one case (843-842). There have been 9 more deaths, for a total of 44. Quest is up another 3,000 tests to over 17,000, which is almost half the tests ever done in the state.

We have not taken to hunting down New Yorkers like the neighbors yet, though we are quarantining visitors to the state. (Presumably Rhode Islanders with homes straddling the state line can travel to the kitchen and back without being quarantined, but they should not hunt New Yorkers while they're here in Massachusetts. Apparently people in distant places like New York disapprove.) Instead, the new sport here is turkey-spotting. They've been seen all over the Boston area, including at the Anna's in Brookline.

In other local news, New Balance is ramping up to produce masks, and the Public Health Commissioner has COVID-19 and so is working from home. Partners hospitals are banning visitors, and a Scituate animal shelter has set up a pet food food pantry.

Day 56: The Herd Strikes Back

Today's title is for Boris Johnson, currently self-quarantining at Number 10 Downing Street.

Do you recall when PlagueBlog did not recommend closing the border to New York State? Well, clearly the governor of Rhode Island is not listening to our recommendations, because she has instituted a house-to-house search for roving New Yorkers, using the National Guard. (This somehow reminds PlagueBlog of the popular theme in Portuguese COVID-19 memes of reconquering a disease-ravaged Spain, or at least Galicia.)

Science Alert suggests that the current coronavirus may be a chimera of a bat coronavirus and a pangolin one.

RaTG13, isolated from a bat of the species Rhinolophus affinis collected in China's Yunan Province, has recently been described as very similar to SARS-CoV-2, with genome sequences identical to 96 percent.

[...]

However, the coronavirus isolated from pangolin is similar at 99 percent in a specific region of the S protein, which corresponds to the 74 amino acids involved in the ACE (Angiotensin Converting Enzyme 2) receptor binding domain, the one that allows the virus to enter human cells to infect them.

By contrast, the virus RaTG13 isolated from bat R. affinis is highly divergent in this specific region (only 77 percent of similarity). This means that the coronavirus isolated from pangolin is capable of entering human cells whereas the one isolated from bat R. affinis is not.

In addition, these genomic comparisons suggest that the SARS-Cov-2 virus is the result of a recombination between two different viruses, one close to RaTG13 and the other closer to the pangolin virus. In other words, it is a chimera between two pre-existing viruses.

P.S. Our numbers are in: Massachusetts is at 3240 cases, up 823 (34%) over yesterday. There were ten more deaths, mostly of patients over 80, for a total of 35. Sex is a growing mystery to the DPH, as is the source of the infection, with over 800 more in the "under investigation" category. Quest has tested 2,800 more patients, more than three times the next runner up (the state lab). A total of seventeen labs (plus "other") are now performing tests.

The commonwealth has officially extended the tax filing deadline to July 15th, and the Governor is on the case of cities who've banned construction.

Also the US has now topped 100,000 cases and 1,500 deaths. New York State is far in the lead with 44,800 cases and 519 deaths.

Day 55: 525,000 Strong

Today the world has exceeded 525,000 cases of the coronavirus we are uniquely not naming after where it came from (well, uniquely except for the other coronavirus from China), with over 23,000 deaths and over 123,000 recovered. With a new high of over 82,000 cases, the US has edged out China for most cases, though not for deaths. Despite underestimating deaths, Italy is still ahead of the viral superpowers with over 8,000 dead. Spain is moving up in the ranks, with second place in deaths and fourth place in cases.

Today's bad news in Massachusetts isn't as bad as yesterday: we are up 579 cases (32%) to 2417, with ten new deaths, mostly among 80-year-olds, for a total of 25. Middlesex still leads the counties; one notable case here is a Market Basket employee in Chelmsford. An Easton Shaw's employee of unknown residence also tested positive.

Failure to trace continues apace, with one more travel-related case, 17 more official local transmission, and over 500 more untraced cases, for a total of over 2000 under investigation. Strangely, a sex unknown category has appeared in the state statistics, with 2 cases. Quest has another 333 positives, out of 2,330 more tested. A fourteenth lab has appeared in the list (BROAD) but without numbers because it is not yet validated.

In the battle over hydroxychloroquine, the Detroit News reports that the governor of Michigan has taken the other side, forbidding doctors from prescribing it off-label. The article is too stupid to explain why, but the restriction is most likely related to a similar one in Ohio meant to guarantee access for patients needing the drug for its on-label purpose (fighting autoimmune disease).

Day 54: Diana's Revenge

Basically everyone on the internet has informed PlagueBlog that Prince Charles has come down with coronavirus, so we're passing it on to you. Take it as you will.

Here in Massachusetts, things have gone from bad to worse, or at least from untested to tested. The total is now 1838 cases, up 679 from yesterday (59%). We also have 4 new deaths, all over 70 and most with pre-existing conditions. The jump is mostly due to testing by Quest, whose numbers have gone up from 379 positive out of over 5,000 tested yesterday to 805 positive out of over 9,000 tested today. The state comes in a distant second with 4,774 tested. LabCorp remains in third place, and the lab count is up to thirteen, plus "other".

P.S. If you're on hydroxychloroquine, PlagueBlog hopes you're also a prepper and stocked up ahead of the rush. Buzzfeed reports Kaiser Permanente is denying hydroxychloroquine prescriptions to lupus patients in California. Also, PlagueBlog recommends against drinking your fish tank cleaner because you don't understand chemistry (or for any other reason).

Day 53: It's a Doozy

I was going to start out with Hong Kong's official report of a second pet case, detected earlier this week in a German Shepherd tested and quarantined on account of its sick owner, but the Massachusetts numbers are out for today and they're a bit much. We are up 382 cases (49%) to 1159, with two additional deaths. Middlesex County alone is over 300 cases, and Essex County is up-and-coming. There are 11 more travel cases, 16 more local transmissions, and an ever-growing backlog with the source under investigation. (Possibly included in the case count for today are the President of Harvard University and his wife; he emailed the community that he got their results back this morning.)

On the bright side, there's a full lab breakdown starting from yesterday, with 12 labs listed (plus, of course, an "other" category). Testing is up 54% over Sunday, with 13,749 tests performed. About 8% have been positive. Though there's been discussion of repeated testing of healthcare workers, this doesn't seem to be reflected in the table.

In case you didn't believe that was the bright side, CTV News reports that Spain has set up a temporary morgue on a Madrid ice rink, as well as field hospitals and military cleaning patrols.

Day 52: Anosmia Joins the Symptom List

Today the world exceeded 350,000 cases, 15,000 deaths, and 100,000 recoveries. Italy is eyeing 60,000 cases, which will be 0.1% of their total population. The US is at 35,000 cases and Spain, a nation of fewer than 47 million souls, is attempting to catch up to us with over 33,000 cases. Germany has pulled ahead of Iran despite their similar populations (around 80 million) and Iran's significant head start. France is falling behind.

In Massachusetts, yesterday's mysterious Duke/Nantucket combined counties case has turned out to be on Nantucket, and the entire island is now sheltering in place. The governor discouraged people from traveling to the islands, then also discouraged the latest fad, traveling across the mainland in search of the ever-more-elusive haircut, by shutting down all non-essential services. FYI: Packies are essential, recreational marijuana dispensaries are not.

One of the more interesting symptoms to emerge from the pandemic is post-viral anosmia or hyposmia, most notably in otherwise asymptomatic patients. If you want to read a bunch of anecdotal reports of the loss of the sense of smell (and therefore of much of the sense of taste), see yesterday's Hacker News thread inspired by the ENT UK post. According to the anecdotal evidence, most people recover their senses eventually.

Also on the science front, last week Cell Discovery finally posted a letter about the efficacy of hydroxychloroquine (a milder form of everyone's favorite repurposed malaria drug, chloroquine) against coronavirus in vitro.

P.S. Today's numbers are in: Massachusetts is at 777 cases total (+131, or 20%), with no new deaths. There were seven more travel cases, 21 more cases of local transmission, and now almost 500 unsourced cases. My county (Middlesex) still leads the pack with 232 cases, well over Boston proper (Suffolk, 154) or anywhere else. Dukes County (Martha's Vineyard) remains free of disease.

Locals should note that besides the state closing for non-essential business tomorrow, indoor gatherings are now limited to 10 persons. Outdoor gatherings are allowed, but I saw a lot of parks padlocked today anyway.

P.P.S. The death count for today is actually 9, up 4 over yesterday. PlagueBlog could swear the PDF said 5 this afternoon. Also, more news sources cannot count the counties of Massachusetts.

Day 51: Next Stop, Italy

The US has reached 30,000 cases, putting us in a firm third place after Italy (53,000) and the source of it all, China (81,000). New York State alone has exceeded 15,000 cases (with 9,000 in New York City alone), leaving all the other states with their impaired testing capacities in the dust. PlagueBlog does not recommend closing the border with New York at this time.

On the plague ship front, The Patriot Ledger reports that hundreds of passengers aboard Germ Boat #15, the Silver Shadow, remain quarantined in the port of Recife (Brazil) after a single passenger tested positive. Despite promises of an airlift out for Americans this weekend, about a hundred remain aboard.

A sister ship, the Silver Explorer, earns Germ Boat #16 status by being in a similar situation off the port of Castro, Chile, after an 85-year old British man disembarked in the south and tested positive in Coyhaique. Silversea Cruises is a subsidiary of Royal Caribbean.

Chile has also refused docking to Germ Boat #17, the Azamara Pursuit, despite its having no verified cases aboard. Other South American ports have refused it entry, and it may need to make the entire 13-day sail back to Miami to offload its (for the moment) healthy passengers. Azamara Cruises is a wholly owned subsidiary of Royal Caribbean.

P.S. Massachusetts' numbers are out for today: 646 cases, up 121 (23%) from yesterday, with 5 deaths (+3). The commonwealth is now providing age ranges on the case numbers. The curve is fairly flat and may be an archive of the testing priorities. Two more cases have been attributed to the Biogen conference, fifteen to travel, fourteen to local transmission, and almost 400 remain unsourced at this time. Positive results are down to 11% for the state lab and up to 7% for the commercial labs.

For some reason the DPH lumped Dukes County and Nantucket County together (with 1 case total), misleading some news outlets into claiming that every county now has a case.

P.P.S. I corrected some number comparisons above.

Day 50: And the Ship Sailed On

The worldwide case count has exceeded 309,000 with over 13,000 deaths. In Massachusetts, today's number is 525 cases, up 112 (27%) from yesterday, with 4 travel-related cases and the remainder due to community spread or not yet sourced. The biggest jumps are in the Greater Boston counties, along with noticeable increases in Essex, Bristol, and Plymouth counties. In a considerable number of cases the county is unknown.

Although not included in today's numbers, Channel 25 reports the death of a Middlesex County woman in her 50's with pre-existing conditions.

Some updates from yesterday: the death in Suffolk County was of an 87-year old Winthrop man. More disturbingly, Channel 25 reported that 9 health care workers at Brigham and Womens and 10 health care worker at Tufts Medical Center tested positive, far exceeding their actual case counts (though not the number of patients pending results at both hospitals). It's not clear how many days of testing this total represents. PlagueBlog is duly alarmed.

On the plague ship front, the numbers have changed yet again for Germ Boat #2, the Diamond Princess, with an eighth death today, a Canadian man in his 70's who had been hospitalized (apparently in Japan). Also some time last week, the Japanese suddenly counted fifteen more positives among ill passengers and their contacts who disembarked before the end of quarantine, bringing the total back up over 700 to 712. The New York Post reported Friday on a study determining that foodservice workers were the nexus of this particular germ boat outbreak.

The New York Times reports on yet another ill-omened cruise aboard Germ Boat #14, the Costa Luminosa. PlagueBlog was surprised by the Princess Cruise yesterday, but always suspected that Carnival Cruise Lines would go on operating its other cruise lines after announcing the apparently quite half-hearted closure of Princess. One of those lines is, of course, Costa Cruises.

The Costa Luminosa sailed out of Fort Lauderdale on February 24th for a Caribbean cruise on which its Italian passengers experienced some issues disembarking, though one Italian passenger was allowed to be hospitalized for an apparently unrelated condition. (He later died of coronavirus.) The ship sailed on out of Fort Lauderdale again, for Europe, reportedly only "half full". A second ill Italian was removed to hospital at a stop along the way. She also eventually tested positive. A comedy of errors ensued with no precautions being taken against the spread of the virus for a week, and then the homemade napkin masks appeared on the waiters.

The US would not permit the ship to dock at its original destination in Italy, so the plan was changed to Marseilles. Several other European ports of call turned the ship away. Yesterday, 400 American and Canadian passengers were finally airlifted home from Marseilles under "harrowing" conditions. Today the plague ship docked in Savona, Italy, despite the country being closed. Italian and Swiss passengers began to disembark; more will disembark tomorrow.

There is so much more news: more plague ships, more disturbing clusters across New England, and a run on chloroquine. PlagueBlog struggles to keep up while also working on a better view of the Massachusetts data.

Day 49: A Quarter Million Strong

Today the international case count has hit 255,000, with 10,000 deaths and almost 90,000 recovered. Italy has over 41,000 cases and 3,400 deaths. Spain has exceeded Iran in cases; both are nearing 20,000. Germany has well over 17,000 cases and the US is approaching 15,000, with 160 deaths.

Today the Treasury Secretary moved Tax Day to July 15th; filing and payment can be delayed without penalty. In a sudden move, Governor Newsom locked down the entire state of California late yesterday with a "shelter in place" order, though marijuana dispensaries and other "essential" businesses will remain open. Pennsylvania is also under a similar order. Massachusetts is still looking good, having dropped to 9th in the nation in case count with no deaths (unlike 28 states and the District of Columbia).

The Internet dug up this gem of a paper from 2007 [PDF]:

[SARS'] acute and dramatic impact on health care systems, economies, and societies of affected countries within just a few months of early 2003 was unparalleled since the last plague. The small reemergence of SARS in late 2003 after the resumption of the wildlife market in southern China and the recent discovery of a very similar virus in horseshoe bats, bat SARS-CoV, suggested that SARS can return if conditions are fit for the introduction, mutation, amplification, and transmission of this dangerous virus.

And lastly, the gift that keeps on giving: plague ships! Lucky Germ Boat #13 is the Ruby Princess, a Princess Cruises ship that (despite Carnival allegedly suspending operations of Princess Cruises a week ago) was still cruising around as late as yesterday when it docked in Sydney. Although thirteen people were ill with flu-like symptoms, the 2,700 passengers were allowed to disembark. Only the ill seem to have been tested; two passengers and one crew member tested positive. Another passenger who travelled to Tasmania has been hospitalized there and is a suspected case.

PlagueBlog trusts this germ boat will continue yielding cases for some time.

P.S. Forbes has an article on the homemade mask movement.

P.P.S Governor Cuomo tweeted his intention to lock down New York State.

P.P.P.S PlagueBlog apologizes for jinxing us: the governor reported the first death in Massachusetts during a press conference this afternoon. The victim was a Suffolk County man in his 80's with pre-existing conditions who died yesterday. The remaining numbers for today are not out yet.

P.P.P.P.S Our numbers are now out. Massachusetts has 413 cases, up 85 (26%) over yesterday, with 17 new cases of local transmission, 15 more travel-related cases, and the remainder under investigation. Middlesex County has 25 new cases, Suffolk 14, Norfolk 12, and Essex 10. Fifty of the new positives were found by the commercial and mystery labs. The state lab positive rate has gone down to 11% while the commercial lab rate has gone up to 5%. (There is still no denominator on the mystery labs.)

Day 48: Lies, Damn Lies, and Statistics

The international case count has exceeded 222,000, with over 9,000 deaths and 84,500 recovered. Italy is approaching 36,000 cases and 3,000 deaths. Iran, Spain, and Germany remain in the teens, and the US, at nearly 9,500 cases and 157 deaths, is now on the wrong side of both France and South Korea.

Massachusetts has dropped to 8th in the nation in case counts. We still have no deaths, though 23 states have at least one already. Many Massachusetts grocery stores have implemented senior hours, and daycare centers will be shut down on Monday, except in certain circumstances involving essential workers.

The Sun Chronicle reports a hospitalized case in Attleboro from an unspecified nursing home, as well as the first case in Mansfield. As of yesterday, there were twelve cases in Southeastern Mass: five cases in Bristol County, five in Plymouth County, two in Barnstable County (the Cape), and none on the islands.

PlagueBlog recommends a New York Times opinion piece from Tuesday about the public health consequences of lying to the public about the need for face masks.

P.S. BBC News reports Italy's death toll has exceeded China's.

P.P.S. Our numbers are out for today: 328 cases total in Massachusetts, up 72 cases (including 4 in Southeastern Massachusetts), with 8 more cases of local transmission, 8 more travel-related, and 56 still under investigation. Hospitalizations went up from 27 to 43 (with a large number still unclassified).

The state lab found 37 of the new positives, the commercial labs (only LabCorp today) found 18, and the underspecified other labs found 17. Total test rates are still unavailable for the other labs, but the state and the commercial labs are still holding at 13% and 4% positive, respectively.