Weekly coronavirus-related chat, questions, and minor updates - week of November 30

Moderna's groundbreaking coronavirus vaccine was designed in just 2 days

On January 11, researchers from China published the genetic sequence of the novel coronavirus. Two days later, Moderna's team and NIH scientists had finalized the targeted genetic sequence it would use in its vaccine.

Bancel downplayed the accomplishment in an interview with the New York Times.

"This is not a complicated virus," he said.

By February 24, Moderna had shipped out its first vaccine batches to NIH scientists in Bethesda, Maryland. Researchers administered the first dose on March 16 in Seattle, Washington. That launched the first clinical trial of any coronavirus vaccine.

But how did they get the sequence?

The Pandemic Heroes Who Gave us the Gift of Time and Gift of Information

Here’s why that date matters: the sequence was published ten days before China acknowledged the severity of the problem by admitting sustained human-to-human transmission and shutting down the city of Wuhan, on January 20th. The sequence was published while China—and the WHO, which depended on China for information—were still downplaying what was going on, in their official statements. The sequence wasn’t published in an official document. Instead, it was published independently in an open-source depository by Yong-Zhen Zhang, a professor at the Shanghai Public Health Clinical Center and School of Public Health.

Zhang had received the virus from Wuhan on January 3rd, around 1:30 p.m., when a metal box continuing a test tube packed in dry ice arrived at his office. The researchers in his team worked feverishly to sequence it over the next two days. Just about 40 hours later, on January 5th at 2 a.m., his team was done.

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It may have taken him a single minute for Zhang to decide, but his bravery was real. This was just 10 days after whistleblowers in Wuhan who had attempted to warn others had been detained by the police. The punishment of these doctors for “rumor-mongering” was broadcast on national TV. Tragically, one of the most prominent whistleblowers, Dr. Li Wenliang, would die of the virus, just a month later (His son was born this summer to his widow). It was a time of silence, not of speaking out. Between January 5th and January 10th, the Wuhan government would not update the number of infected people. It would be another 10 days before the dam broke and President Xi Jinping made his first public statement, saying “the virus must be taken seriously.”

Sadly, the hammer did come down fast. Zhang’s lab was immediately shut down for “rectification”—an obscure term to imply some “malfeasance,” as the South China Morning Post explains.

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At the end of February, the South China Morning Post was reporting that Zhang’s lab was still shut down. Things did improve, though. Dr. Zhang continues to carry out important work—and has been recognized with awards.

So we've hit just about a month with zero new cases, zero deaths (one yesterday, first in a month) and I think no active cases. It's very exciting! Been a long hard road to get here. But everything's opening up again, carefully. Things are mostly under control interstate and in NZ too.

A covid testing site in Los Angeles will be shut down for a day...in order to film a movie

And it's not even going to be a good movie.

“He’s All That,” which features the TikTok star Addison Rae and is a reboot of the 1999 romantic comedy “She’s All That”

edit: and there's the backpedaling

Canada PM Trudeau indicates U.S. border restrictions to last a long time

Canada will not agree to lifting a ban on non-essential travel with the United States until the coronavirus outbreak is significantly under control around the world, Prime Minister Justin Trudeau said on Tuesday.

Trudeau’s comments were a clear indication that the border restrictions will last well into 2021. The two neighbors agreed to the ban in March and have rolled it over on a monthly basis ever since.

Usual personal update:

The school building I'm in had 20 confirmed cases this week. Not my whole school district -- my specific school building.

With students and staff together we number well under 1000 people total.

State, district, and local leadership all continue to oppose a shutdown.

The UK has approved a COVID-19 vaccine, but the US is still waiting. Here's why.

Regulators in the US and the UK do things differently: The FDA asks drugmakers for raw data, which it reanalyzes itself, while British regulators rely more heavily on reports produced by the drugmakers.

Not really news, but The Beaverton (Canada's version of The Onion) has been killing it lately:
Santa Claus states fake Pandemic won’t stop him from entering anyone’s home
Conservative Party slams Trudeau for not doing enough to combat anti-vaxxers in Conservative Party
Brian Pallister eagerly awaits Amazon order for pandemic response plan
Health Canada warns of inevitable “spring wave” of terrible COVID-inspired Fringe plays
Government reassures Canadians who ran out of EI they are still eligible for “Call Your Parents” benefit
Jason Kenney’s pride now leading cause of death in Alberta

I’m 33 Years Old. I Got COVID-19 Eight Months Ago. I’m Still Sick.

I’m 33 years old. Before I got sick with COVID-19 in April, I was traveling nonstop for my work as a campaign reporter, with 12- to 14-hour days on my feet, sometimes working 10 or more days in a row. In between all that, I’d fit in hot yoga classes and jogs every couple of days.

The best way I can describe how I am now, at the end of this strange, horrible year, is that I wake up most days feeling like I drank a six-pack of beer the night before. Washing the dishes, doing my laundry, or walking a few blocks leaves me in need of a sit-down. It’s a sort of gritty feeling in my body, a woolly feeling in my brain. My breathing is up and down; when I'm tired, I forget words midsentence. I need at least 10 hours of sleep most nights. And if I push too hard, it’s not just laborious — it’s actually painful, from my lungs to my head to the stinging in my eyes.

COVID-19 has forced me to reevaluate how I think about health, work, vulnerability, and strength. And I’ve wondered whether the pandemic will force our culture at large to make some reevaluations, too. Maybe it will force us to question the American cult of individualism, that idea that doing well or being well is solely down to a person’s willpower. Maybe it will finally make clear that we’re not, as the ads at the beginning of the lockdowns said, “all in this together,” and that our failure to think about collective health and responsibility means many, many people fall through the cracks in a crisis.

Inside a hospital as the coronavirus surges: Where will all the patients go?

With more than 91,000 covid-19 patients in their beds, U.S. hospitals are in danger of buckling beneath the weight of the pandemic and the ongoing needs of other sick people. In small- and medium-size facilities like this hit hardest by the outbreak’s third wave, that means finding spots in ones and twos, rather than adding hundreds at a time as New York hospitals did when the coronavirus swept the Northeast in the spring.

Santa Clara Co. says it may run out of hospital beds by mid-December

Santa Clara County says the surge in COVID-19 patients they are seeing is "gravely concerning" and that they may run out of hospital capacity in a little more than a week. ICU capacity in hospitals serving the Eastern and Southern parts of the county has filled to 93% -- those are the hardest hit areas. County officials are imploring residents to avoid gatherings, wear masks, and put off unnecessary travel. The county also said it has submitted its plan to the state about how to distribute a COVID-19 vaccine. The plan calls for the first doses to be directed towards frontline healthcare workers. A mandatory 14-day quarantine order went into effect over the weekend for people arriving to the county after travel.

Also:

Nearly 200 Santa Clara County retailers fined for social distancing fails

Santa Clara County slapped fines on 181 retailers over the Thanksgiving holiday weekend for failing to properly notice social distancing requirements, worsening the pain for many shop owners already struggling after months of coronavirus restrictions.

The inspections came as a surprise to many of the 427 stores that county inspectors visited over the weekend, with offenders ranging from giant warehouse retailers like Costco to tiny boutiques like Pinkberry yogurt shop at Stanford Shopping Center.

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County officials said they netted more than $115,000 in fines, ranging from $250 to as much as $3,750 each, during their “enhanced Black Friday COVID-19 Business Compliance effort” that concluded Sunday. Fines may continue to accrue daily until businesses correct the violations and submit a compliance statement.

“Business compliance with the mandatory directives in the health officer’s risk reduction order is a critical element of our COVID-19 response,” said Michael Balliet, director of the county’s business compliance and enforcement unit.

The top three violations were failure to submit a social distancing protocol, failure to properly post the required social distancing protocol signage and failure to post the required capacity signage, county officials said. Those documents, officials said, help the public and employees understand what the business must do to comply with the mandatory directives and keep their workers and customers safe.

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County officials last week had announced the crackdown before the holiday began, stressing that they would issue fines on the spot rather than their usual approach of working with businesses to correct violations.

Alberta asks federal government, Red Cross for field hospitals as COVID spreads

A federal source with direct knowledge of the situation says Alberta has asked the federal government and the Red Cross to supply field hospitals to help offset the strain COVID-19 is having on the health-care system.

The source said Alberta would likely receive at least four field hospitals — two from the Red Cross and another two from the federal government. The source, speaking on condition of confidentiality, said there was no request for human resources to staff the hospitals and no request for support from the military.

Covid’s Cassandra: The Swift, Complicated Rise of Eric Feigl-Ding - a look at Eric Feigl-Ding, who's become one of the major "coronavirus influencers" on Twitter, going from about 2000 followers to almost 350,000 now because of his tweets during the pandemic.

Austin, Texas mayor stressed residents ‘need to stay home.’ He was vacationing in Cabo San Lucas at the time.

In early November, as health officials warned of an impending COVID-19 spike, Austin Mayor Steve Adler hosted an outdoor wedding and reception with 20 guests for his daughter at a trendy hotel near downtown.

The next morning, Adler and seven other wedding attendees boarded a private jet for Cabo San Lucas, Mexico, where they vacationed for a week at a family timeshare.

One night into the trip, Adler addressed Austin residents in a Facebook video: "We need to stay home if you can. This is not the time to relax. We are going to be looking really closely. ... We may have to close things down if we are not careful."

CDC advisory panel’s lone dissenter on why long-term care residents shouldn’t receive Covid-19 vaccine first

All the U.S.-based Phase 3 trials of Covid vaccines have to include people 65 and older. But none has specifically tested the vaccines in people who are in long-term care. One can’t assume findings in people over age 65 who are healthy enough to be accepted for a clinical trial are indicative of everyone in that demographic, she said.

At an earlier ACIP meeting, Talbot warned that vaccinating this population at the start of the vaccine rollout is risky, because long-term care residents have a high rate of medical events that could be confused as side effects of vaccination and undermine confidence in the vaccines. “And I think you’re going to have a very striking backlash of, ‘My grandmother got the vaccine and she passed away,’” she said at the time.

[....]

Do you have any safety concerns about use of the vaccine in long-term care residents?

Any more than anyone else? No. But I think what we have for the adult population in general is a randomized control trial to look at the safety data.

What do you mean?

If something happened to me following the vaccine, we could go back to the randomized control trial data and look at did this happen in both groups? Did happen in the placebo group or not. We can’t do that for the long-term care facility because there wasn’t a trial done in the long-term care facility.

Photos: The Reality of the Current Coronavirus Surge

As the number of cases of COVID-19 worldwide nears 65 million, and the number of deaths attributed to the disease approaches 1.5 million, many countries are enduring a crushing surge in numbers. The toll on health-care workers, families, and the victims of the disease has been enormous. Gathered below are photographs from around the world of the current battle against COVID-19, taken over the past few weeks.

As Covid-19 spikes again, Monterey health officials have some dire predictions

Yesterday, Dec. 1, when the Monterey County Board of Supervisors convened, representatives of each of Monterey County’s four hospitals weighed in with sobering updates. While beds and equipment like ventilators are just fine, staffing is the biggest challenge. And the Covid patient population in Monterey County’s hospitals is now roughly double its previous record. “It’s really stressing our capacity, frankly,” Dr. Allen Radner, Chief Medical Officer of Salinas Valley Memorial told the supervisors.

“We’re really concerned that over the next month or two the numbers are just going to worsen,” he said. “This is real, this is serious. People that don’t believe this—I wish they could take a tour of our hospital. Most of the people on ventilators are in their 50s, with no known pre-existing medical problems.”

How a Llama and a University of Texas Lab Led to the Most Promising COVID-19 Treatment Yet

On Tuesday, the world’s largest multidisciplinary scientific society, the American Association for the Advancement of Science, named the recipients of its annual Golden Goose Awards. The honor recognizes scientific breakthroughs that start in unusual places—like a vial of blood from a llama named Winter, whose antibodies have proven critical in the development of new treatments for COVID-19, including the drug Bamlamivimab.

A new statistic shows that health-care workers are running out of space to treat COVID-19 patients.

In August and September, about 9.5 percent of COVID-19 cases were admitted to hospitals nationwide [...] In the last week of October [...] [l]ess than 8 percent of those cases made it into the hospital, a 16 percent drop [...].

Ultimately, only 7.4 percent of COVID-19 cases were hospitalized in November—the lowest percentage yet.

This change may not seem ominous at first. You might expect to see such a divergence, for instance, if testing rapidly increased, so that states were suddenly detecting many more mild cases of COVID-19. But the data don’t show any evidence of this kind of “casedemic”—if anything, they show the opposite. Last month, the number of total COVID-19 tests increased by about a third compared with October, but the number of total cases discovered more than doubled. More people are getting sick.

At the same time, the virus seems to be killing a slightly higher fraction of people diagnosed with it.

Yes, coronavirus testing works. But not in the way you might expect.

The high rate of false negatives means that testing provides the most protection when it’s deployed at the population level. At the group level, it’s only a weak, adjunct tactic to other precautions. And at the individual level, it’s borderline useless.

Bride with Covid-19 gets married in quarantine

(Shared for the picture. Reminds me of Pushing Daisies.)

Vaccines against SARS-CoV-2 will have side effects – that’s a good thing

To make vaccines more effective, whole labs have been dedicated to the testing and development of new adjuvants. All are designed with the same basic purpose – to kick the immune system into action in a way that maximizes the effectiveness and longevity of the response. In doing so, we maximize the number of people that will benefit from the vaccine and the length of time those people are protected.

To do this, we take advantage of the same sensors that your immune system uses to sense damage in an active infection. That means that while they will stimulate an effective immune response, they will do so by producing temporary inflammatory effects. At a cellular level, the vaccine triggers inflammation at the injection site. Blood vessels in the area become a little more “leaky” to help recruit immune cells into the muscle tissue, causing the area to become red and swell. All of this kicks off a full-blown immune response in a lymph node somewhere nearby that will play out over the course of weeks.

In terms of symptoms, this can result in redness and swelling at the injection site, stiffness and soreness in the muscle, tenderness and swelling of the local lymph nodes and, if the vaccine is potent enough, even fever (and that associated generally crappy feeling).

This is the balance of vaccine design – maximizing protection and benefits while minimizing their uncomfortable, but necessary, side effects. That’s not to say that serious side effects don’t occur – they do – but they are exceedingly rare. Two of the most discussed serious side effects, anaphalaxis (a severe allergic reaction) and Guillain-Barré Syndrome (nerve damage due to inflammation), occur at a frequency of less than 1 in 500,000 doses.

Some vaccine-related stuff I've been reading today:

• The Trump administration pledged several hundred million vaccine doses in 2020. Companies will actually ship about 10 percent of that
• An alarming number of Americans say they'd reject a COVID-19 vaccine, posing a risk to the country's ability to achieve widespread immunity (including over half of surveyed NYC firefighters saying they wouldn't get vaccinated)
• A neat little thing on the NY Times site that estimates where "in line" you'd be for a vaccine (for non-US people, you can just enter a random county name in an area you're interested in)

And also:

• Rudy Giuiliani has tested positive - he's 76 and does not seem healthy, so he's probably at significant risk.

New CRISPR-Based Test for COVID-19 Uses a Smartphone Camera

In a new study published in the scientific journal Cell, the team from Gladstone, UC Berkeley, and UCSF has outlined the technology for a CRISPR-based test for COVID-19 that uses a smartphone camera to provide accurate results in under 30 minutes.

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Not only can their new diagnostic test generate a positive or negative result, it also measures the viral load (or the concentration of SARS-CoV-2, the virus that causes COVID-19) in a given sample.

“When coupled with repeated testing, measuring viral load could help determine whether an infection is increasing or decreasing,” says Fletcher, who is also a Chan Zuckerberg Biohub Investigator. “Monitoring the course of a patient’s infection could help health care professionals estimate the stage of infection and predict, in real time, how long is likely needed for recovery.”

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In the new test, the Cas13 protein is combined with a reporter molecule that becomes fluorescent when cut, and then mixed with a patient sample from a nasal swab. The sample is placed in a device that attaches to a smartphone. If the sample contains RNA from SARS-CoV-2, Cas13 will be activated and will cut the reporter molecule, causing the emission of a fluorescent signal. Then, the smartphone camera, essentially converted into a microscope, can detect the fluorescence and report that a swab tested positive for the virus.

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“We hope to develop our test into a device that could instantly upload results into cloud-based systems while maintaining patient privacy, which would be important for contact tracing and epidemiologic studies,” Ott says. “This type of smartphone-based diagnostic test could play a crucial role in controlling the current and future pandemics.”

(So, not actually available. This is announcing that the paper got published with the results of their study.)