Weekly coronavirus-related chat, questions, and minor updates - week of November 1

Got my COVID booster today at a Walgreens, was in and out in 30 min. I originally had the J&J back in April, this one was the Moderna. So far no side effects, we'll see how I feel in the morning.

The Economist - The number of people who have died from covid-19 is likely to be close to 17m

(everything but the main graph is paywalled, so here is the article text)

WHEN COVID-19 first hit northern Italy in February 2020, The Economist noticed that something strange was happening. There were 1,140 deaths attributed to the virus in parts of Bergamo province in March, for example, but the overall increase in fatalities compared with the same period in the previous year was 2,420. Similar phenomena were soon noticed in America, Britain, Spain and other countries.

Official covid death tolls were—and continue to be—inaccurate. They typically rely on testing for the virus, which can be patchy, and use definitions which exclude indirect consequences of the pandemic, such as extra deaths in overburdened hospitals. Fortunately, there is a better way to calculate death tolls. To measure those of events such as wars, researchers do not check how many dead people have bullets in them, but on something much more reliable: how many more died during them than one would expect in normal years. This is known as “excess deaths”.

The gulf between official and reliable counts of covid-related deaths means that while the global toll officially passed 5m on November 1st, the actual number of people lost to the virus is, by The Economist’s count, closer to 17m.

Undercounts are much more significant in poorer countries. In Bulgaria, pandemic deaths are probably nearly twice as high as the official tally. In Russia, the official statistics seem to underestimate the true number of covid deaths by a factor of 3.5; in India the government’s number underestimates the death toll by a factor of ten. As well as leading to a poor understanding of the virus’ true spread, this phenomenon means that the pandemic’s impact is underestimated most in the countries with the least resources to fight it (see map).

There are still some reasons to use the official death counts. They can show trends over time within countries, for example. But too often they are used to compare rich and poor countries or to assess the global death toll—metrics for which they are useless. They are still used, however, because they are more up to date than excess-death counts, and, unlike them, are available for all countries.

The Economist has found a way to remedy this situation, and is the only source of daily updated estimates of excess deaths around the world. To find the true death toll of the pandemic, The Economist first collected mortality data for all countries where it was available (with help from researchers and volunteers), and then built a machine learning model to predict it where it is unknown. (We have made these estimates, as well as our data, code and models, freely available, and presented our work to the World Health Organisation, among others.) Our estimates, at time of writing, find the most likely global death toll to be 16.8m, with a confidence interval of between 10.3m and 19.5m. The likeliest date for when deaths due to the pandemic passed 5m fell in the first week of December 2020.

Our model estimates come with uncertainty, sometimes enormous, especially in the places with the least data available. But uncertainty around a correct number is both warranted and appropriate when data are imperfect. It is also better than the alternative: full confidence in a single number, that is certain to be wrong.

COVID proteins that trigger strokes and heart attacks identified by Israeli team

The scientists made the discovery by taking a “peek in the virus’s black box,” Dr. Ben Maoz of Tel Aviv University told The Times of Israel, explaining that his team analyzed all 29 proteins of the virus to figure out which of them are wreaking havoc in the vascular system.

“Coronavirus isn’t the purely respiratory disease we first thought, and we have identified the proteins that put patients at increased risk of stroke, heart attack, and other problems associated with the vascular system,” Maoz said.

He identified the five proteins in SARS-CoV-2 that lead to vascular problems in the peer-reviewed journal eLife.

“This work could well help scientists to develop drugs to counter the effect of the coronavirus on the vascular system, by providing an understanding of exactly which proteins, or pieces of the virus, are causing problems,” said Maoz.

His lab, which focuses on biomedical engineering and neuroscience, collaborated with other Tel Aviv University departments to create a simulation of a human vascular system and observe the impact of all 29 coronavirus proteins. From their analysis, they were able to identify which of them affected the vascular system — and how.

“We have not only discovered which proteins have an impact on the vascular system, but also seen how exactly they exert their effect,” said Maoz. “What we found is these specific proteins make your vasculature more leaky. The tubes become more porous and cannot hold liquid as you would hope. This information is also valuable in efforts to develop drugs.”

Maoz hopes to lay foundations for more nuanced treatment of coronavirus.

Link to the study:
https://elifesciences.org/articles/69314

got a Moderna booster today, after getting J&J back in April.

here in Seattle they've converted a giant Amazon meeting hall into a vaccine assembly line on the weekends. wonderfully smooth process. I registered online, and was in & out in less than 30 minutes total.

a heartwarming little detail: most of the people getting vaxxed seemed to be kids because of the new eligibility rules. so in the observation area afterwards where they make sure you don't have an allergic reaction, they had a woman dressed as Snow White reading a kids book, and Batman going around and taking pictures with kids.

Pfizer says COVID-19 pill cut hospital, death risk by 90%

On Friday, Pfizer released preliminary results of its study of 775 adults. Patients who received the company’s drug along with another antiviral shortly after showing COVID-19 symptoms had an 89% reduction in their combined rate of hospitalization or death after a month, compared to patients taking a dummy pill. Fewer than 1% of patients taking the drug needed to be hospitalized and no one died. In the comparison group, 7% were hospitalized and there were seven deaths.

“We were hoping that we had something extraordinary, but it’s rare that you see great drugs come through with almost 90% efficacy and 100% protection for death,” said Dr. Mikael Dolsten, Pfizer’s chief scientific officer, in an interview.

Study participants were unvaccinated, with mild-to-moderate COVID-19, and were considered high risk for hospitalization due to health problems like obesity, diabetes or heart disease. Treatment began within three to five days of initial symptoms, and lasted for five days. Patients who received the drug earlier showed slightly better results, underscoring the need for speedy testing and treatment.

Pfizer reported few details on side effects but said rates of problems were similar between the groups at about 20%.

An independent group of medical experts monitoring the trial recommended stopping it early, standard procedure when interim results show such a clear benefit. The data have not yet been published for outside review, the normal process for vetting new medical research.

Here’s Why Rapid COVID Tests Are So Expensive and Hard to Find in the US (ProPublica)

Companies trying to get the Food and Drug Administration’s approval for rapid COVID-19 tests describe an arbitrary, opaque process that meanders on, sometimes long after their products have been approved in other countries that prioritize accessibility and affordability over perfect accuracy.

[...]

In late May, WHPM head of international sales Chris Patterson said, the company got a confusing email from its FDA reviewer asking for information that had in fact already been provided. WHPM responded within two days. Months passed. In September, after a bit more back and forth, the FDA wrote to say it had identified other deficiencies, and wouldn’t review the rest of the application. Even if WHPM fixed the issues, the application would be “deprioritized,” or moved to the back of the line.

“We spent our own million dollars developing this thing, at their encouragement, and then they just treat you like a criminal,” said Patterson. Meanwhile, the WHPM rapid test has been approved in Mexico and the European Union, where the company has received large orders.

An FDA scientist who vetted COVID-19 test applications told ProPublica he became so frustrated by delays that he quit the agency earlier this year. “They’re neither denying the bad ones or approving the good ones,” he said, asking to remain anonymous because his current work requires dealing with the agency.

FDA officials said they simply want to ensure that rapid tests detect even low levels of the virus, since false negative test results could cause people to unwittingly spread the disease. They blame the test shortages on an absence of the kind of sustained public funding that European governments have provided. Without it, manufacturers have lacked confidence that going through the FDA’s process would be financially worth the trouble.

[...]

Recognizing the potential market for antigen tests, companies began submitting more EUA applications in late 2020. But the FDA was wary about this type of test, mostly warning of the danger of false negatives in the earliest stages of infection.

FDA officials were particularly concerned about allowing tests to be administered outside the purview of a trained health care provider. “To mitigate the impact of false results, all Covid-19 tests authorized to date have been made available only by prescription, so that clinicians can interpret results for patients,” wrote Shuren and his deputy Dr. Tim Stenzel in an October 2020 column in The New England Journal of Medicine.

That cautious approach persisted all through the winter and early spring, despite rising agitation from the White House and Congress around the availability of tests.

“I actually have been saying that for months and months and months, we should be literally flooding the system with easily accessible, cheap, not needing a prescription, point of care, highly sensitive and highly specific” tests, White House chief medical advisor Dr. Anthony Fauci said under questioning from Schrier in a hearing on March 17.

[...]

The FDA reviewer who quit this May described what the delays looked like from the inside. With a background in virology, he could evaluate the hundreds of pages in an application within a few days. But then, something strange happened: The applications would go nowhere for months as higher-up officials seemed paralyzed by indecision.

“I could easily process dozens of them, but I ended up with one or two in my queue constantly. They would stay there forever,” he said. “I had a lot of free time.”