Leiter Reports: A Philosophy Blog

New COVID worries: the new Brazilian and South African variants of the coronavirus

Here; an excerpt

The more transmissible variant, B.1.1.7, is already spreading rapidly in the United Kingdom, Ireland, and Denmark, and probably in many other countries. But scientists are just as worried about 501Y.V2, a variant detected in South Africa. Some of the mutations it carries, including ones named E484K and K417N, change its surface protein, spike, and have been shown in the lab to reduce how well monoclonal antibodies combat the virus. In a preprint published earlier this month, Jesse Bloom, an evolutionary biologist at the Fred Hutchinson Cancer Research Center, showed that E484K also reduced the potency of convalescent sera from some donors 10-fold—although he is quick to add this does not necessarily mean the mutation would cause people's immunity to the new strain to drop 10-fold.

P.1 [the Brazilian variant] adds to the concerns because it appears to have hit on a similar constellation of mutations and has emerged in a place with a high level of immunity. “Anytime you see the same mutations arising and starting to spread multiple times, in different viral strains across the world, that's really strong evidence that there's some evolutionary advantage to those mutations,” Bloom says....

(Thanks to Dr. David Ozonoff for the pointer.)

Efficacy of Pfizer and Moderna vaccines on the new variants of the coronavirus

This paper suggests the vaccine is likely to need updating at various intervals for maximum effectiveness.  If that's right, it means the current mass vaccinations which are just getting started may need to be undertaken again next fall.  If I'm misunderstanding the paper, or if readers have links to other helpful information about this issue, please comment, below.

(Thanks to Bob Matthews for the pointer.)

Lectures recorded because of COVID that might be available to the public?

Reader Neil Webb writes:

One of the consequences of Covid is that lectures have been delivered online.

While many of those lectures will only be available to students within an institution some are available to anyone with internet access.

Would you mind asking those who do have lectures available and are happy for them to be shared more widely to provide a link so that others can benefit from them?

As I explained to Mr. Webb, often these lectures can not be shared outside the university (that is the rule here, for example).  Often student privacy rights under FERPA are implicated in sharing recordings, another obstacle.   But readers can post links to lectures being recorded during COVID that are widely available (maybe there is already an archive with such links somewhere?).

Can people vaccinated for COVID still be contagious?

A nicely done news article about what we do and don't know at this stage.   From the conclusion:

In the end, the vaccines likely limit transmission in two ways:

 

1. Preventing some percentage of infections totally, even asymptomatic ones. This prevents the body from replicating the virus and having enough to share with others.

 

2. Turning a further percentage of what would have been symptomatic infections to asymptomatic ones, thus preventing the body from coughing, sneezing and generally shooting the virus long distances.

 

Overall, I think it would be reasonable to estimate that vaccines reduce transmission from anywhere from 30% to 90% — a huge range, to be sure, but it depends on the vaccine used and the accuracy of these studies with limited sample sizes.

 

That result would be both good and bad. On one hand, it’s not total sterilizing immunity — someone who has been vaccinated still has a reasonably high likelihood of picking up the disease at a party and giving it to their immunocompromised friend later in the week. That means the vaccinated probably shouldn’t go to parties where there are unvaccinated people while the pandemic rages.

Why is the new variant of the coronavirus more transmissible (if it is)?

It's been hard to find a clear answer to this in the media.   The most common surmise I've seen is that the new variant reproduces more in the nose and throat, and so people expel more of it when they sneeze or cough.   But a recent NYT article suggests these as possible explanations:

In a typical coronavirus, the tip of the spike protein is like an ill-fitting puzzle piece. It can latch onto human cells, but the fit is so loose that the virus often falls away and fails to infect the cell.

The N501Y mutation seems to refine the shape of the puzzle piece, allowing a tighter fit and increasing the chance of a successful infection....

One mysterious [additional] mutation in the B.1.1.7 lineage [of the coronavirus] deletes the 69th and 70th amino acids in the spike protein. Experiments have shown that this deletion enables the coronavirus to infect cells more successfully. It’s possible that it changes the shape of the spike protein in a way that makes it harder for antibodies to attach.

I'd be curious to know what other accounts of the mechanism readers have seen.  I'll conclude with observations by longtime reader Dr. David Ozonoff from the Boston University School of Public Health, with whom I've corresponded a bit about this:

I don’t think we know how (or truthfully even whether) the virus is more transmissible. Transmission is very complicated and depends on characteristics of the host (us), the environment (social behavior, season, etc.) and the virus itself. The evidence so far available does suggest increased transmission is very plausible but I don’t believe the evidence is ironclad (but it doesn’t have to be). In this context the exact mechanism (which is what you seem to be seeking) is just speculative and increased viral load is a reasonable speculation. Increased affinity for the ACE-2 receptor and increased infectivity of younger age groups has also been mentioned. I don’t think we can say what the exact mechansm or mechanisms is/are at work here.

UPDATE:  Dr. Ozonoff just sent along this informative new article from the generally excellent STAT.

New study suggests COVID immunity appears to be longlasting

An account here; an excerpt:

Covid-19 patients who recovered from the disease still have robust immunity from the coronavirus eight months after infection, according to a new study....

[T]he new study does show that a small number of recovered people do not have long-lasting immunity. But vaccination ought to offset that problem by ensuring herd immunity in the larger population. 

The new paper studied blood samples from 185 men and women who had recovered from covid-19—most from a mild infection, although 7% were hospitalized. Each person provided at least one blood sample between six days and eight months after their initial symptoms, and 43 of the samples were taken after six months. The team that ran the investigation measured the levels of several immunological agents that work together to prevent reinfection: antibodies (which tag a pathogen for destruction by the immune system or neutralize its activity), B cells (which make antibodies), and T cells (which kill infected cells). 

More on the allocation of scarce medical resources during the pandemic, and a lack of consensus among bioethicists about how to proceed

Bioethicist Thomas Cunningham (Loyola Marymount Bioethics Institute) writes:

Thanks as always for your continued commentary and wise read of the news of interest to the world and to philosophers, broadly conceived.

Sometime around March, you discussed allocation of scarce resources in US hospitals on your blog. At that time I suggested there was a consensus in the bioethics community about how to do this. I am writing today to revise my assessment, as this is very much in the news and may remain of interest to you and your readers.

Here in Los Angeles, we are experiencing absurdly low supplies for various resources. Speaking generally, and not about my health system in particular, I am aware of shortages in ventilators, machines that deliver high concentrations of oxygen to patients, oxygen itself, hemodialysis machines, feeding pumps, IV machines, the lines that they require to deliver therapies to patients, and other equipment. Hospitals are also seeing such unprecedented volumes of hospitalized patients that they have considered implementing triage protocols to allocate patients to lower levels of care that have adequate staffing, as reported here.

Which states are treating college teachers as "essential workers" (like K-12 teachers) for vaccine purposes and which aren't

This article is informative.

Los Angeles today is Northern Italy in March and April

A chilling account from the Los Angeles Times.

Fomites are not driving this pandemic

We've touched on this topic before, but more recent work confirms the earlier suspicion:

If a person infected with the coronavirus sneezes, coughs or talks loudly, droplets containing particles of the virus can travel through the air and eventually land on nearby surfaces. But the risk of getting infected from touching a surface contaminated by the virus is low, says Emanuel Goldman, a microbiologist at Rutgers University.

"In hospitals, surfaces have been tested near COVID-19 patients, and no infectious virus can be identified," Goldman says.

What's found is viral RNA, which is like "the corpse of the virus," he says. That's what's left over after the virus dies.

"They don't find infectious virus, and that's because the virus is very fragile in the environment — it decays very quickly," Goldman says....

Scientists now know that the early surface studies were done in pristine lab conditions using much larger amounts of virus than would be found in a real-life scenario.

How the Pfizer and Moderna vaccines work

An illuminating (if sometimes challenging) discussion by biologist Jerry Coyne (Chicago).

Another useful document for the "war crimes" trials for Trump and the others who led America to disaster in the "war" on COVID

A gripping narrative from USA Today.

(Thanks to Gregory Pence for the pointer.)

Pfizer and Moderna vaccines compared...

...in an article by Helen Branswell, a very good and reliable journalist at StatNews.   Some interesting details that I had not seen elsewhere (e.g., the minimum size of an order of the Pfizer vaccine is much larger than for Moderna, which will no doubt affect what entities, and where, order each).   It is unlikely any of us will have a choice as to which vaccine we get.

COVID vaccine tracker: how many shots, and where (for the US)

Courtesy of Bloomberg.

*Early* symptoms of COVID: some differences by age

This is a useful compilation and visualization of some data on symptoms in the first seven days of a COVID infection.

The road to "herd immunity" without, and with, a vaccine

Interesting set of calculations--note that if two-thirds of the population in the U.S. takes the vaccine, we could reach herd immunity by the summer of 2021.  Without any vaccine, and this disaster would continue into 2025!

Statins and COVID

We noted many months ago the possibility that statins (which reduce cholesterol) may help prevent severe cases of COVID.   Now research from UC San Diego confirms this and reveals a possible mechanism.  (One of the few things we know about Trump's health history is that he takes statins, by the way; whether that played a role in his fairly short bout with COVID is unknown, of course.)

Moderna vaccine for COVID will also be approved...

...meaning that, with the Pfizer vaccine, the U.S. should have enough vaccine to innoculate 100 million people by the end of March 2021. 

ADDENDUM:  Some more details on the Moderna vaccine:

Moderna previously disclosed clinical trial data showing that 185 cases of Covid-19 occurred in those who received a placebo injection, which was given to half the volunteers in its 30,000-person study. Just 11 cases occurred in those volunteers who received the vaccine.

Signs of the COVID times in the academy at some Connecticut public universities

Fortunately, faculty at Southern, Central, Eastern and Western Connecticut State Universities are represented by a union, which they will need given the start of these negotiations:

A draft contract put forth by the university eliminates procedural protections regarding academic freedom, terminations and retrenchment; faculty ownership of original online course materials and the right to teach them; conference, travel and research funds; universitywide tenure committees; and privacy and grievance policies for personnel files.

The university system also wants to increase teaching loads from 12 credit hours per semester to 15 and pilot changing the academic calendar from two to three terms, with faculty members required to teach for two such terms annually.

If you know of similar cases of proposals for radical cuts and restructuring in the wake of the pandemic, feel free to add links in the comments.

FDA approval being sought for rapid COVID test using saliva...

...developed by researchers at Tulane University.   Are there other such tests being considered by the FDA?  Information and links welcome.

(Thanks to Edward Johnson for the pointer.)

Find your "place in line" for a vaccine in the U.S.

A useful interactive tool.

(Thanks to Gregory Pence for the pointer.)

What is wrong with people in Boise, Idaho?

They're watching too much Fox TV I guess, but this is still grotesque:

In Boise, Idaho, public health officials about to vote on a four-county mask mandate abruptly ended a meeting Tuesday evening because of fears for their safety amid anti-mask protests outside the building and at some of their homes.

One health board member tearfully announced she had to rush home to be with her child because of the protesters, who were seen on video banging on buckets, blaring air horns and sirens, and blasting a sound clip of gunfire from the violence-drenched movie “Scarface” outside her front door.

“I am sad. I am tired. I fear that, in my choosing to hold public office, my family has too often paid the price,” said the board member, Ada County Commissioner Diana Lachiondo. “I increasingly don’t recognize this place. There is an ugliness and cruelty in our national rhetoric that is reaching a fevered pitch here at home, and that should worry us all.”

Vaccine update

The Pfizer vaccine is very effective, the Oxford/AstraZeneca vaccine only moderately so.   Since the UK government got its act together to purchase large amounts of the Pfizer vaccine, we'll find out in the next month or two whether there are any rare side-effects (the second dose of the Pfizer vaccine does seem to produce modest side-effects in most patients--some mix of fever, chills, aches).

Another ominous sign for New York's post-COVID future

Goldman Sachs looking to move some of its operations to Florida or Texas.

Signs of the COVID times in the academy: cuts, cuts, cuts

At the University of Colorado, Boulder:  "[W]e propose to rebalance the ratio of tenure-track faculty to instructors. Currently, that ratio, by head count, is 3.3:1 (TTT to instructors). Reducing tenure-track faculty by 50 and adding 25 instructors would yield a new ratio of 2.8:1. Accounting for related savings, making this move would free $6.2 million annually."  [Instructors typically teach 4/4 loads, rather than 2/2 loads.]

At the University of Vermont:  The "plan would terminate majors including Geology, Religion, Asian Studies and several language programs such as Greek, Latin and German. Minors in many of these subject areas would also be cut, plus others in Theatre and Vermont Studies. Master’s programs to be cut include Greek & Latin and Teaching Latin, Geology and Historic Preservation.  The plan would wipe out the college’s Classics, Geology and Religion departments. Other departments would be consolidated."  Some tenure-stream faculty may lose their positions altogether.

ADDENDUM:  And wealthy private universities are offering financial incentives for faculty to retire.  Yale is offering up to 200K for faculty who retire by next summer, while I know Penn is offering two years of salary as a retirement incentive to certain senior faculty to retire by next summer (for faculty in the professional schools this could amount to 750K or more).

COVID isolation periods should be shorter

Peak infectiousness is in the two days before symptoms start, and for five days thereafter.  From the article:

In September, France dropped its required period of isolation to seven days from 14 days, and Germany is considering shortening it to five days. (Isolation refers to people who are ill; quarantine refers to people who have been exposed to the virus and may become ill.)

Masks work against the coronavirus...

...and cloth masks work better than other kinds.  (Full study here.)

When will the COVID pandemic end?

McKinsey, the business consultants, say probably in the third quarter of 2021 (July-September), maybe as late as the 4th quarter of 2021.  Their reasoning seems sensible enough.

Mask-wearing: the Danish study

This study has gotten some attention, but the media accounts I've seen don't accurately report what it found (this one is typical).  First, the study did not control at all for what participants did and who they were with when not outside the home:  so it is possible that the participants (who wore masks outside the home) lived with folks who never wore masks and/or did careless things that exposed them to infection.  Second, the study also did not control for exposure to non-mask-wearers outside the home.  One possible takeaway from the study is that wearing surgical masks (the masks at issue) is not very effective when you're around others who are not wearing surgical masks as well, which seems plausible.

Wuhan after the lockdown

An interesting study; among the findings of note:

(1)  "All city residents aged six years or older were eligible and 9,899,828 (92.9%) participated. No new symptomatic cases and 300 asymptomatic cases (detection rate 0.303/10,000, 95% CI 0.270–0.339/10,000) were identified."

(2) "The detection rate of asymptomatic positive cases was very low, and there was no evidence of transmission from asymptomatic positive persons to traced close contacts. There were no asymptomatic positive cases in 96.4% of the residential communities.  Previous studies have shown that asymptomatic individuals infected with SARS-CoV-2 virus were infectious³, and might subsequently become symptomatic⁴. Compared with symptomatic patients, asymptomatic infected persons generally have low quantity of viral loads and a short duration of viral shedding, which decrease the transmission risk of SARS-CoV-2⁵. In the present study, virus culture was carried out on samples from asymptomatic positive cases, and found no viable SARS-CoV-2 virus. All close contacts of the asymptomatic positive cases tested negative, indicating that the asymptomatic positive cases detected in this study were unlikely to be infectious."

(I came across this via the Twitter feed of the word's dumbest journalist, Alex Berenson, who (1) didn't realize that the study shows, among other things, that lockdowns work, something dumb-dumb likes to deny [how could they not work, we know how the virus is transmitted, and it requires people to come into contact with other people; that doesn't mean lockdowns are also worth the costs]; and (2) dumb-dumb also declared that the study shows that, "Asymptomatic spread isn’t real = masking healthy people is useless," but the study shows nothing of the kind:  it shows that asymptomatic people who don't go on to develop symptoms appear not to infect others; as the study notes, we have evidence that asymptomatic people who go on to develop symptoms are infectious.)

Oxford/AstraZeneca vaccine: 70% effective on average

Another two-dose vaccine, that was 90% effective in the group that got a half-dose first, and then a full dose second (but less effective in the group that got a full dose each time).  Note that in this trial they also checked for asymptomatic infections.   Various experts comment here.

North Dakota leads the world...

...in recent deaths per capita from COVID.  1 out of every 1,000 residents has died from COVID.  Unsurprisingly, North Dakota has done very little in the way of mitigation efforts throughout this catastrophe.

The Governor of California should resign

What a disgrace.  It's pretty easy not to have a dinner in a restaurant while people are dying from an infectious disease and you're requiring everyone else to not do this.   He should be crucified for this selfish stupidity.

What is wrong with the people in Farmington, Missouri?

Their local public health official  received threats because she is trying to implement simple measures to reduce the spread of COVID.  It got so bad, she resigned and moved.  Farmington is about 75 mile from St. Louis.  What is wrong with the people there?  I hope to God I never have to set foot in that place, or any place so benighted.

The latest on the Pfizer vaccine...

...from Statnews.  Between Pfizer and Moderna's vaccine, it looks like about 6-7% of the U.S. population may get vaccinated before the end of the year, which is better than nothing of course.  Hopefully by summer, it will be possible to vaccinate most of the population that wants it (states can mandate vaccinations, and hopefully some will, with exceptions only for health reasons).

Still to be determined, of course, is how long the protective effect of the vaccine lasts.  Does anyone know of any preliminary data or informed estimates?

The Moderna COVID vaccine

MOVING TO FRONT FROM YESTERDAY--SEE COMMENT BY NED BLOCK, WHICH NOTES A SERIOUS POSSIBLE OMISSION IN THIS STUDY

An informative report from Statnews:

The Moderna vaccine reduced the risk of Covid-19 infection by 94.5%. There were 95 cases of infection among patients who received placebo in the company’s 30,000-patient study. There were only five infections in patients who developed Covid-19 after receiving Moderna’s vaccine, mRNA-1273....

Moderna also released data about the number of patients who had severe Covid-19. There were 11 cases of severe disease, all of them in the placebo group — another point of encouragement for Fauci.

“There was always the concern … since the primary endpoint [of the trial] is just clinically apparent disease, how do we know it’s going to have an impact on severe disease? And the results with severe disease were striking — 11 to zero is very impressive,” he said. At the time of their data release, Pfizer and BioNTech had no severe cases in their study...

More on the Swedish COVID disaster: the "herd immunity" that wasn't

Here.  Of course, the Swedish disaster isn't as bad as the American one, but that's not saying much!

Mobility network models of COVID

People going to gyms and restaurants means trouble,  among other findings.

COVID vaccine and the universities

Next fall may be normal, but masks will probably be necessary through the Spring.

Mink-strain of COVID spreading to humans?

I don't know whether this is pure alarmism or whether it has some factual basis and we should worry.  Any insight from readers?

Promising initial data on Pfizer vaccine for COVID

The NYT story includes the appropriate notes of caution as well.   If it's 90% effective, that's phenomenal.  That it has proven safe in 43,000 people is good but does not yet mean it is really safe.  If it produces adverse effects in 1 out of every 100,000 people, they might not yet know, but that level of risk would produce thousands of adverse cases just in the U.S.  It would still be worth distributing such a vaccine in all likelihood.

Small Boston study finds 1 in 5 grocery store workers test positive for COVID

But the vast majority were asymptomatic.  Given that clerks in a grocery store will interact with several dozen people during a day, and in a closed environment, this isn't wholly surprising, but still sobering if it generalizes.  All the more reason to mask up carefully when grocery shopping.

AI to spot "COVID cough"?

This is interesting, although I do wonder whether by the time the "cough" is detectable, a person has not already been infecting lots of others.

(Thanks to Robert Condlin for the pointer.)

How the coronavirus spreads through a room, a bar, a classroom

Nice visuals.

Meanwhile the COVID disaster rolls on

Over 9,000 new confirmed cases in Chicago over the last week, the highest recorded number ever (the previous high, last Spring, was over 7,000, but that surely wildly undercounted, as Chicago was doing about 25% of the daily testing that's being done now).   On the other hand, Cook County, where Chicago is, is averaging about 30 cases per 100,000, well below other parts of Illinois which are closer to the neighboring disaster areas, especially Wisconsin, but also Iowa and Missouri.

What a fiasco the Trump Virus has been.  Apart from Bolsonaro, we couldn't have had a worse national leader during this world-historic event.

Another university succeeding despite COVID

This time Cornell University--but, in typical journalistic hysteria-mongering, the article treats this as "rare" rather than the norm.

Coronavirus infection: it's not just the nose, it's also importantly the mouth!

This is interesting.

(Thanks to Dr. David Ozonoff for the pointer.)

Hospitals in Utah preparing to ration care...

...due to surge of COVID patients.   Utah has a 7-day rolling average of about 1,400 cases per day in a population of a bit more than 3 million.  By way of comparison, Illinois has a 7-day rolling overage of about 4,100 cases per day, but with a population four times the size; Illinois is, not yet, facing such a crisis, but Illinois also has a fairly good ratio of beds to persons compared to many other states.  (Illinois has 2.8 ICU beds per 10,000 people, while Utah has 2.2.)

As COVID cases surge, one bit of good news is that doctors are now much better at averting death

A useful overview of the changes:

Two new peer-reviewed studies are showing a sharp drop in mortality among hospitalized COVID-19 patients. The drop is seen in all groups, including older patients and those with underlying conditions, suggesting that physicians are getting better at helping patients survive their illness....

The study, which was of a single health system, finds that mortality has dropped among hospitalized patients by 18 percentage points since the pandemic began. Patients in the study had a 25.6% chance of dying at the start of the pandemic; they now have a 7.6% chance.

That's a big improvement, but 7.6% is still a high risk compared with other diseases....

 

Horwitz and her colleagues looked at more than 5,000 hospitalizations in the NYU Langone Health system between March and August. They adjusted for factors including age and other diseases, such as diabetes, to rule out the possibility that the numbers had dropped only because younger, healthier people were getting diagnosed. They found that death rates dropped for all groups, even older patients by 18 percentage points on average....

COVID on campus: an update

Philosopher Gregory Pence (Alabama/Birmingham) kindly shared this list of universities with the biggest outbreaks of COVID on campus.  What they have in common is that they are all large, mostly state schools, most of which have big fraternity/sorority scenes.  (One surprise on the list is BYU, which is large, but is an alcohol-free campus, which one would have expected to contribute to more sensible behavior by students.)   But these schools are the outliers, as even the NYT data reveals, despite their best journalistic effort to emphasize the negative:

More than 35,000 cases [COVID] cases have been identified since early October.

Though some colleges moved all their fall classes online, many campuses remained open even as positive tests accumulated by the hundreds or thousands. Of more than 1,700 institutions surveyed by The Times, more than 50 reported at least 1,000 cases over the course of the pandemic. More than 375 colleges have reported at least 100 cases.

Translated into non-hysterical English:  3% of universities account for about a third of all the cases on campuses, and one-quarter of the schools account for almost all the cases--meaning about 70% of colleges and universities are doing quite well.  Considering that COVID is spreading out of control in huge parts of the country, colleges are performing admirably overall.