Leiter Reports: A Philosophy Blog

Vaccines and the Delta variant, and what lies ahead for America

Informative Twitter thread from a physician at the University of California, San Francisco; an excerpt:

If you’re fully vaxxed, I wouldn’t be too worried, especially if you’re in a highly vaxxed region....

[U]nvaxxed may well do OK for a while, probably through summer [due to the large number of vaccinated people]. But fall/winter now scares me a lot, much more than it did 2 weeks ago....

[F]or Delta, Pfizer dose 1 is only ~33% protective. https://gov.uk/government/news/vaccines-highly-effective-against-b-1-617-2-variant-after-2-doses This creates 2 problems: 1) People stay vulnerable until after shot 2 (& many let guard down earlier); 2) Loss in efficacy for dose 1 points to some degree of vaccine/immune escape. And – though this isn’t proven – I’d worry that a fully vaccinated elder, or someone whose immunity stems from an infection >12 mths ago, won’t be sufficiently protected over time, if immunity falls below a threshold needed to thwart Delta....

More on the COVID lab leak hypothesis

This looks to be a balanced evaluation of the evidence; bottom line is that the evidence doesn't rule out a leak from a virology lab, but the evidence is also compatible with a natural origin.

(Thanks to Dr. Roger Albin for the pointer.)

Sign of the COVID times...

...Chicago reported only 62 new cases of COVID in the entire city yesterday--that's by far the lowest daily total since testing began more than 14 months ago.

Did the coronavirus escape from a virology lab in Wuhan?

Here's a detailed and sober abductive argument that it did, although it's not conclusive.

(Thanks to Roger Crisp for the pointer.)

List of colleges now requiring students and/or employees to be vaccinated

At CHE.

How effective are the COVID vaccines?

Really effective.  (There's more at biologist Jerry Coyne's blog, where I first saw this.)

COVID indoor safety guidelines

This is interesting (it allows you to calculate risk and "best practices" for different scenarios).

(Thanks to Jeff Roland for the pointer.)

American College Health Association recommends all colleges mandate vaccination for COVID before fall enrollment

This is obviously sensible, and will give ammunition to schools in benighted states who will no doubt face opposition from local politicians of a certain flavor.  Colleges already mandate vaccinations for many illnesses, the only thing new here is the disease.

(Thanks to Jeff Roland for the pointer.)

Excess mortality due to COVID (directly or indirectly)

Useful representation of the data by sociologist Kieran Healy (Duke).

What the experts still want to know about COVID and the virus that causes it

Alas, there's still a lot to learn, from how long immunity lasts, to how variants will affect vaccines, to why some suffer "long COVID" while others don't even develop symptoms.

(Thanks to Dean Rowan for the pointer.)

University of California and California State University systems will require COVID vaccine as condition of enrollment...

...as well they should.  Every university in the country should follow suit, although I'm sure public universities in benighted states will face obstacles.

(Thanks to Robert McGarvey for the pointer.)

UPDATE:  And now the University of Maryland.  (Thanks to Peter Carruthers for the pointer.)  Feel free to add more in the comments.

Bolsonaro's crime against humanity

What a despicable monster.

Pfizer vaccine less effective against South Africa variant

UPDATE:   The news article misreports the results, probably because the lab itself communicates so poorly (you have to skip all the way down to #6 in the tweet thread for the point to finally be made clear).  In fact, there were no cases of infection by the South African variant two weeks after the second dose!  The variant did better than expected at infecting people before that time.  So, in fact, once fully faccinated, Pfizer is highly protective even against the South African variant!  Both the journalists and the lab deserve the blame here for poor communication of the results.  (Thanks to Matthew Noah Smith for calling my attention to this.)

Although how much less effective we still don't know:

A team from Tel Aviv University and the Clalit healthcare organization sequenced the swabs of 150 Israelis who tested positive for COVID-19 despite having been vaccinated.

In their study, the prevalence of the South African strain among vaccinated individuals who were infected despite their inoculation was eight times higher than its prevalence in the unvaccinated infected population. Though the number of such infections among the vaccinated was relatively small, the findings indicated that this variant was far more successful in getting through vaccinated individuals’ defenses than other strains.

“Based on patterns in the general population, we would have expected just one case of the South African variant, but we saw eight,” Prof. Adi Stern, who headed the research, told The Times of Israel....

The research, which has been posted online but not yet peer-reviewed, is likely to raise questions about Pfizer’s own real-world study, which found that in South Africa, despite the local strain being prevalent, the vaccine was 100 percent effective.

More good news about the Pfizer and Moderna vaccines

Here; an excerpt:

A new study suggests the messenger RNA vaccines produced by Moderna and the Pfizer-BioNTech partnership appeared to be 90% effective in preventing Covid-19 infection in a real-world setting....

The study followed nearly 4,000 health care workers, first responders, and other essential workers in eight U.S. locations as the first Covid vaccines were rolled out starting in December. Participants were tested weekly to look for all cases of Covid infection, even asymptomatic ones.

In the period from Dec. 14, 2020, to March 13, 2021, nearly 75% of the workers in the cohort received at least one dose of one of the mRNA vaccines...

Informative news article comparing COVID vaccines

Here.  All the vaccines are quite good, but Pfizer and Moderna results are really quite remarkable.

Rutgers University announces that COVID vaccination will be required for all students for enrollment next fall

Good for them.  They will give medical and (unfortunately) religious exemptions.  Other colleges and lower schools should follow suit.

(Thanks to Robert McGarvey for the pointer.)

"How dangerous are the new COVID variants?"

This is an informative journalistic piece, that also explains the mechanisms in virtue of which the variants are more contagious.

Vaccines should be able to end the pandemic, despite new variants

So say some Harvard researchers (let's hope they're right!):

“What we’re seeing is that these variants don’t seem to affect T-cell immunity all that much and they [the T-cells] seem to be as effective in recognizing these variants as they do the original virus,” [Harvared medicine professor] Alter said. “What that means is that we actually have very important backup mechanisms built into our vaccines that will continue to provide protection against these newly emerging variants.”

A case of reinfection with the South African variant of the coronavirus

The patient was much sicker the second time.  Alarming, and hopefully anomalous.

(Thanks to Jason Brennan on FB for the pointer.)

The future of COVID: short-term, medium-term, long-term

Informative, as usual, from STAT News.

McGill University announces return to in-person classes in fall 2021

Here.  Have other schools already announced fall plans?  Feel free to include links to announcements in the comments.

The "California variant" of the coronavirus

Reasons to be worried?   Links to better-informed discussions of this development welcome.

UPDATE:   This article is quite misleading; see the link in the first comment.

New study out of the UK on the impact of the Pfizer and AstraZeneca vaccines on serious illness

This is welcome news:

Research led by Public Health Scotland found at four weeks after the first dose, hospital admissions were reduced by 85% and 94% for the Pfizer and AstraZeneca jabs respectively.

It is the first sign of the real world impact of vaccination in the UK.

Figures for England are expected to be released later.

Among the over 80s, there was an overall 81% reduction in the numbers admitted to hospital.

COVID herd immunity by April in the U.S.?

Although this appears on the opinion page of the Wall Street Journal, the author is not a crank, but a serious medical professional at Johns Hopkins; an excerpt:

Cases are down 77% over the past six weeks. If a medication slashed cases by 77%, we’d call it a miracle pill. Why is the number of cases plummeting much faster than experts predicted?

In large part because natural immunity from prior infection is far more common than can be measured by testing. Testing has been capturing only from 10% to 25% of infections, depending on when during the pandemic someone got the virus. Applying a time-weighted case capture average of 1 in 6.5 to the cumulative 28 million confirmed cases would mean about 55% of Americans have natural immunity.

Now add people getting vaccinated. As of this week, 15% of Americans have received the vaccine, and the figure is rising fast. Former Food and Drug Commissioner Scott Gottlieb estimates 250 million doses will have been delivered to some 150 million people by the end of March.

There is reason to think the country is racing toward an extremely low level of infection. As more people have been infected, most of whom have mild or no symptoms, there are fewer Americans left to be infected. At the current trajectory, I expect Covid will be mostly gone by April, allowing Americans to resume normal life.

There's more detail in the essay.  Is this assessment plausible?

More on COVID and Vitamin D3

From the abstract of a forthcoming article in The Lancet:

Our study aims to elucidate the effect of calcifediol [25(OH)D3] treatment on ICU admission and mortality, in patients admitted to COVID-19 wards of Hospital del Mar, Barcelona, Spain. A total of 930 participants were included. Participants (n=551) were randomly assigned to calcifediol treatment (532 ug on day one and 266 ug on day 3, 7, 15, and 30) at the time of hospital admission or as controls (n=379).

Findings: ICU assistance was required by 110 (11.8%) participants. Out of 551 patients treated with calcifediol at admission, 30 (5.4%) required ICU, compared to 80 out of 379 controls (21.1%; p<0.0001). Logistic regression of calcifediol treatment on ICU admission, adjusted by age, gender, linearized 25(OH)D levels at baseline, and comorbidities showed that treated patients had a reduced risk to require ICU (RR 0.18 [95% CI 0.11;0.29]). Baseline 25(OH)D levels inversely correlated with the risk of ICU admission (RR 0.53 [95% CI 0.35;0.80]). Overall mortality was 10%. In the Intention-to-treat analysis, 36 (6.5%) out of 551 patients treated with calcifediol at admission died compared to 57 patients (15%) out of 379 controls (p=0.001). Adjusted results showed a reduced mortality for more of 60%. Higher baseline 25(OH)D levels were significantly associated with decreased mortality (RR 0.40 [95% CI 0.24;0.67]). Age and obesity were also predictors of mortality.

Interpretation: In patients hospitalized with COVID-19, calcifediol treatment at the time of hospitalization significantly reduced ICU admission and mortality.

(Thanks to Joshua Selby for the pointer.)

South Africa finds the Oxford/AstraZeneca vaccine doesn't even prevent mild illness very well from the new variant there

This is alarming, especially for UK citizens, where this vaccine has been widely used.   Readers?

COVID vaccines and the new variants

Bad news and good news; an excerpt:

Even if the vaccines are less powerful against the [South Africa] variant, they still appear to protect people from the worst outcomes, like hospitalization or death. But the loss in efficacy against the B.1.351 [South African] variant in clinical trials suggested to some experts that the immunity the shots confer may not last as long against that form of the coronavirus. Or that the vaccines won’t be as powerful of a drag on transmission, the way scientists hope the shots will be for other versions of the virus.

Trouble for Australian universities without international students?

This is ominous; an excerpt:

“My sense is that international education in Australia is in deep, deep trouble. That means higher education is in deep trouble and scientific research is in equally deep trouble, because this is heavily financed from international student fees.”

Marginson, a former professor of higher education at the University of Melbourne, said, “There is now a major forking of the way” between the British and Australian higher education systems, because Australia has closed its borders during the pandemic, while Britain has not, as well as the greater dependence on international student fees and weaker public science funding in Australia.

“My political nose tells me that [Australia’s] government is not greatly worried about the declining position of university science and still less about the overall position of universities in Australia. It knows that the decline of international education means that the economy will take a hit, but with this government, politics comes before economics,” Marginson said.

Comments are open for additional links or information from those more knowledgeable about the situation.

Does the AstraZeneca/Oxford vaccine *really* reduce transmissibility of the virus?

The headlines have been claiming that, but the reality is more complicated and less clear.

All the COVID vaccines appear to prevent serious disease and death

And that's pretty important, even if people may still get stick.  An excerpt:

Here’s the key fact: All five vaccines with public results have eliminated Covid-19 deaths. They have also drastically reduced hospitalizations. “They’re all good trial results,” Caitlin Rivers, an epidemiologist at Johns Hopkins University, told me. “It’s great news.”

Many people are instead focusing on relatively minor differences among the vaccine results and wrongly assuming that those differences mean that some vaccines won’t prevent serious illnesses. It’s still too early to be sure, because a few of the vaccine makers have released only a small amount of data. But the available data is very encouraging — including about the vaccines’ effect on the virus’s variants.

 

What the National Football League (U.S.) learned about COVID

Here.  Infection can occur with contact as little as five minutes.  Masks make a difference, being outdoors makes a difference.  Sharing vehicles, eating together:  not a good idea!

A guide to the new coronavirus variants

This is quite informative.

(Thanks to Dean Rowan for the pointer.)

Another COVID study: for Pfizer 2-dose vaccine, majority can still be infected after just one shot

Here; the crucial bit: 

Last week, Israel released preliminary data on the effects of vaccination for infection. Early indications suggest that after vaccination, as many as 70% of people can still be infected by SARS-CoV-2 after the initial dose of the Pfizer vaccine. More data is needed to confirm the effects on transmissibility among the vaccinated. 

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

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

MOVING TO FRONT FROM JANUARY 21--SOME INTERESTING CONTRIBUTIONS IN THE COMMENTS,  MORE WELCOME

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?).

Vaccines are working: the case of Israel

Three weeks after the first shot, there's been a 60% drop in hospitalizations for those sixty years old or over.  Israel has been vaccinating aggressively and more quickly than most countries.

ADDENDUM:  An article appeared today in the NYT about Israel and the vaccine with additional details.

Brace yourselves: we may be years away from not worrying about the coronavirus

The South African variant is leading major vaccine makers to update their vaccines.   We are, I suspect, looking at at least yearly vaccines to protect against this virus.   Perhaps, as with influenza, vaccines that are not wholly effective will nonetheless protect against serious illness and mortality from the virus.   I'm as hopeful as the next person that the current vaccinations, which are just barely beginning in the U.S., will dramatically reduce mortality.   But I fear we are a very long time away from "normal" life. 

Using images to persuade COVID skeptics

Philosopher Nathan Ballantyne (Fordham) and others discuss.

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.)

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.