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

Rural community in shock after Georgia raids clinic vaccinating teachers

A small Georgia city was still in shock Friday, days after state health workers raided the busiest medical clinic in the county and seized its Covid-19 vaccine supply because staffers had given doses to teachers.

In addition, the George Department of Public Health said it would not be providing any more vaccines to the medical center for the next six months until July 27.

County schools have been open because many of the 3,000 or so children enrolled in the district don’t have internet service, which would allow for virtual learning, and also rely on the schools for food, clinic Dr. J. Daniel McAvoy told the newspaper.

"So we saw it as very important to get our school teachers vaccinated, and stepped out and did that," McAvoy said. "And then we saw the guidance later."

Early on, Poon said, they invested $7,000 out of their own pockets on an expensive freezer capable of storing the vaccines because they wanted to be part of pandemic solution.

Usual personal update:

There is no update. We’re in a holding pattern. We will continue this way, for months, until vaccines permeate the population. There isn’t any other strategy. There never was.

Local numbers are actually trending down right now, which feels great, but it’s really only good in a relative sense. We’ve been so habituated to high numbers that weeks that would have been unheard of just a few months ago now feel like relief because at least they’re not as bad as our worst.

Also, everyone’s steam has run full out by now. School is a joyless place. My students, my coworkers, and I are all shells of individuals. We sit in separated silence much of the time. Enthusiasm is rarely expressed and, when it is, feels faked or forced. I hate seeing my students like this, but I’m powerless to do anything about it. They hate seeing me like this, and they too are powerless.

District administration has pretty much stopped notifying us or anyone of positive cases. At the beginning of this a note went home to parents for every single positive case that was in the building. That stopped only a few weeks in, as the frequency of letters started to get alarming. I’ve stopped wondering if COVID is in my class on any given day and just assume that it is at this point. My school of less than 1000 has had 60+ cases so far, and those are only ones that we know about. A lack of mandatory testing and well as local testing being unable to keep up with demand both point to the actual number being far higher.

I know I sound bitter, and I undoubtedly am, but in the same way that I can look at our local numbers and find happiness from a relative perspective rather than dread from an absolute one, I’m actually quite grateful for my situation. I hear horror stories about teachers elsewhere. Our district still enforces six feet of separation, requires masks for everyone, and bought us air filters (underpowered ones, but filters nonetheless). I know of schools that are doing none of those things. I know of schools who think that you’re meant to pick one mitigation strategy instead of using them in tandem. I know of schools where teachers and administrators still openly believe that this is a hoax.

My situation is not ideal, but when I compare my situation to the available landscape, I consider myself lucky to be in the position that I am. I think that says something about the low watermark our national response to COVID has set.

I think this is going to be my last update here. I don’t like dwelling on this any more than I have to, especially because it’s clear nothing is going to change. My goal is simply to stay COVID-free for the next few months until I can get the vaccine. The likelihood of me making that stretch without getting it is low, and at this point is pretty much out of my control. Every day is simply a roll of the dice as to whether the mitigation strategies work. I’ve been lucky so far, and I don’t think there’s really anything more for me to say unless they don’t work. If I test positive I’ll let everyone know, but until then, consider no news from me to be good news.

Thanks to everyone who has read my updates over the months and cared about my situation. This has been a really tough road (not just for me but for everyone) and this place has been great for me in making that path a little less lonely and difficult.

The Brazil variant is exposing the world’s vulnerability

Even in a year of horrendous suffering, what is unfolding in Brazil stands out. In the rainforest city of Manaus, home to 2 million people, bodies are reportedly being dropped into mass graves as quickly as they can be dug. Hospitals have run out of oxygen, and people with potentially treatable cases of COVID-19 are dying of asphyxia. This nature and scale of mortality have not been seen since the first months of the pandemic.

Manaus saw a devastating outbreak last April that similarly overwhelmed systems, infecting the majority of the city. Because the morbidity was so ubiquitous, many scientists believed the population had since developed a high level of immunity that would preclude another devastating wave of infection.

Though many questions remain, one plausible explanation is that people who have already been infected by the virus are getting sick—and not mildly so. That possibility has been long feared throughout the pandemic, yet not previously seen on any significant scale. It comes at a time when variants of SARS-CoV-2 are being identified around the world, including a report in Minnesota of a case of the variant that has become dominant in Brazil. Although no known variants have been found to pose an immediate threat to vaccinated people, the capacity for reinfection to any significant degree would reshape the pandemic’s trajectory.

U.S. Reaches Deal With Australian Company for At-Home Covid-19 Tests

That's great and all, but "19 million tests a month by the end of the year" would have been great if this was any time last year. Rapid daily testing would have been a huge help for containing the virus last year. By the end of this year we'll have hopefully achieved vaccine-driven herd immunity. Some extra testing while the vaccine is still being distributed is better than nothing though.

Chicago teachers say they won’t put their families at risk by returning to the classroom

Includes a heartbreaking picture of Dwayne Reed teaching a virtual class outside in the Chicago winter as a protest against going in to the school building.

Biden health team hatches new vaccine strategy as variant threat builds

Shots made yearly to battle the flu rely on a foundational vaccine that is then altered to fight the particular variants that pop up each season. Drawing from flu vaccine practices would mean that manufacturers could skip monthslong trials that enroll thousands of people and instead prove safety and effectiveness in smaller studies that track a few hundred volunteers for weeks.

[...]

Adapting the flu strategy is an approach championed by scientists. It’s not practical to run full-fledged late-stage trials for Covid-19 booster shots or revised vaccines, said Paul Offit, a vaccine expert at the University of Pennsylvania who sits on FDA’s vaccine advisory board.

UK coronavirus variant gets nastier as South African variant spreads

Coronavirus variants are becoming increasingly concerning as they mutate. Samples of the more transmissible B.1.1.7 coronavirus variant, which was first detected in the UK, have acquired a mutation that will help them evade immune protection – the same mutation already present in the B.1.351 variant in South Africa, which is now spreading worldwide.

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With many countries doing little or no sequencing, it is likely that the B.1.351 variant is more widespread than these figures suggest. According to Björn Meyer at the Pasteur Institute in France, when the city of Cologne in Germany started doing a lot more sequencing, it found that 5 per cent of coronavirus infections were due to the B.1.351 variant, revealing that the virus was already well established.

Our world in data has a massive factsheet on how COVID vaccination is going.

I found these 4 charts (and 1 map) the most important:

Share of people fully vaccinated against COVID-19 (AKA "back to brunch day" countdown chart, absent fully/highly effective anti-vaccine COVID mutations)

COVID-19 vaccination policy

Share of people that have gotten at least 1 COVID vaccine

Daily COVID doses administered per 100 people (known and stored?)

Cumulative/Total COVID vaccines worldwide

I would have liked 2 more charts telling us how many people are getting vaccinated each day unfortunately.

Israel’s decision to give 5,000 vaccine doses to Palestinian health workers is wholly inadequate, rights group says

Israeli Defense Minister Benny Gantz’s office announced that the transfer had been approved on Sunday, marking the first such move since the country of 9 million began receiving shipments of the Pfizer-BioNTech vaccine in mid-December.

Israel has since then deployed what’s become the fastest vaccination campaign in the world in terms of shots per person.

Rights organizations say the lack of equitable vaccine distribution to Palestinian territories is a dereliction of duty by Israel, which is classified by the U.N. as an occupier state.

“Israel retains overriding control over land, over the population registry, over the movement of people and goods, over airspace. So under international law, that sort of control comes with it, obligations towards an occupied population,” Shakir said

Israeli officials argue that ultimate responsibility for health services and vaccine acquisition falls upon the Palestinian Authority, which is elected by Palestinians to govern the West Bank.

The mystery of the missing vaccines

State and local officials bristle at being accused of hoarding or mismanagement, and given any chance at all they’ll turn the subject to the supply line. They say they are delivering shots as fast as they can, and as soon as the spigots open, they’ll deliver even more. They say vaccine sites being too conservative about storage should be easing up now that the Biden administration has told them how much they can expect and when over three weeks. A few told me that some health care facilities had more staff than they initially anticipated turn down the shot — but that more of them are now baring their arms as they’ve watched their coworkers get inoculated without harmful effects. So their inventory gaps are closing.

But it’s also clear that the coronavirus vaccine tracking system is barely a system. Sometimes hospital workers enter the vaccination in a patient’s electronic medical record — without understanding that it doesn’t connect to the state vaccine registry. Sometimes second doses are double-counted. Sometimes a vaccine distribution site “batches” the data, meaning they do it every few days, not in real time, so it looks like there are more discrepancies. Some reports are “delayed or missing,” the Association of State and Territorial Health Officers executive director Mike Fraser acknowledged in a press call today.

And sometimes it’s just the delivery schedule. Vaccines aren’t delivered to states every day — so, Shah said, if you have appointments scheduled for Monday, but you aren’t getting another shipment until Wednesday, you can’t use them all up on Sunday. The “gap” waxes and wanes.

Fixing the data systems isn’t going to happen over night. But as the Biden administration asserts, cautiously, that the vaccination drive is getting better, some of the psychology of vaccine hoarding may have already begun to dissipate. State officials are telling providers not to hold back — more is on the way. “Let me worry about getting you the second doses,” Shah said he tells them. “ Do not keep them on the shelves.”

Russia's Sputnik V vaccine is 91.6% effective against symptomatic Covid-19, interim trial results suggest

After criticism last year for an early rollout, Russia's Sputnik V vaccine is 91.6% effective against symptomatic Covid-19 and 100% effective against severe and moderate disease, according to an interim analysis of the vaccine's Phase 3 trial results.

The preliminary findings were published in The Lancet on Tuesday and are based on data gathered from 19,866 participants, of which around three-quarters (14,964) received two doses of the vaccine and a quarter (4,902) were given a placebo.

[...]

The vaccine is already approved in Russia, Belarus, Serbia, Argentina, Bolivia, Algeria, Venezuela, Paraguay, Turkmenistan, Hungary, UAE, Iran, Guinea, Tunisia, Armenia and the Palestinian territories. Sputnik V has so far been administered to more than 2 million people worldwide.

Zeynep says that You Should Take Any Vaccine.

For most of these trials, our “endpoint” has been things like any disease, however minor, even sniffles. Even when we look at “severe” disease, it isn’t what most of us think of as severe: hospitalization, ICU, ventilation and such.

So what’s the news there? Since the beginning of the trials, all trials, there has not been a single death or hospitalization among people vaccinated. Not one. Zero. Not for Moderna, not for Pfizer/BioNTech, not for Oxford/AstraZeneca, not for Sputnik, not for J&J, not for Novavax.

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The reason I emphasize this is that there is a mismatch between what the trials measure, which is “any disease”—because it is a better metric to get us where we need to arrive quickly—and the metrics we should be concerned about for purposes of public health and ending this pandemic. The public conversation around it has been less than productive, comparing the “efficacy” numbers, as if they had much clinical significance. Is one vaccine better than the other? I’ve even seen doctors—with tens of thousands of social-media followers—advocate that a rich country should aim to procure one of the “more efficacious” ones, basically treating the others as inferior.

The president wants to reopen the nation’s schools during the dawn of his term, but labor-strong California is putting such hopes in serious jeopardy.

Newsom, who normally measures his words and maintains a controlled public persona, last week boiled over and told local superintendents they should give up hope of reopening this school year if “everybody has to be vaccinated.” In a meeting inadvertently streamed on YouTube, the governor lost his cool and said, if nothing gives, they might as well tell the “truth” to parents: “There will be no in-person instruction in the state of California.”

The vast majority of California's 6 million public schoolchildren haven't seen a classroom since coronavirus shutdowns in March. California's sky-high infection rates this winter, coupled with a long history of empowering local teachers and district officials, have made school reopening a non-starter in most cities. That has run headlong into a vaccine release that is desperately short on supply while giving teachers the expectation they should receive shots before they return.

“I am now concerned about the opening of schools in August 2021,” Natomas Unified Superintendent Chris Evans recently told state lawmakers. “California is largely at a standstill.”

[...]

Newsom and Biden are walking an increasingly thin political tightrope, juggling demands from those unions with those from frustrated parents and concerned education advocates who want schools open now.

Teachers say they, too, are tired of distance learning. But they assert the risks are too high — that they will get the virus or bring it home to a loved one. California's infection rates have fallen in recent weeks, but they were among the highest in the nation in December and early January, enough to force stay-at-home orders across most of the state.

Meanwhile, teachers point to the spread of new variants said to be more contagious. They wonder how they can teach a mix of students in person and online, since some families are likewise wary of returning. And they have been given few explanations so far of how they can receive vaccines, even though Newsom has repeatedly said they are eligible.

Israel's vaccine rollout linked to infection fall

Israel's vaccination programme is showing signs of working to drive down infections and illness in the over-60s.

The fall appears to be most pronounced in older people and areas furthest ahead in their immunisation efforts.

This suggests it is the vaccine, and not just the country's current lockdown, taking effect.

On Twitter, here are some graphs.

The New Yorker has a long read that's primarily about the Russian vaccine, but also helps for understanding the science behind other vaccines that take a similar approach.

The Sputnik V Vaccine and Russia’s Race to Immunity

Sputnik V—like several other covid-19 vaccines, developed by Oxford University and AstraZeneca, in the United Kingdom; CanSino Biologics, in China; and Johnson & Johnson, in the United States—is what is known as a vector vaccine. This type of vaccine is much newer than the attenuated or inactivated kind but has a longer track record than the mRNA variety. In the nineties, scientists began exploring the use of disabled viruses as “vectors,” or carriers for implanting genetic material into human cells. Early experiments focussed on therapies for hemophilia and cystic fibrosis, among other genetic diseases. Soon, pharmaceutical companies and scientific centers around the world began looking into the potential application of the technology for vaccines. As Konstantin Chumakov, a Russian-American virologist who is an adviser to the World Health Organization and a member of the Global Virus Network, an international coalition that tracks viral pathogens, explained, the vector is “a Trojan horse to go in and deliver whatever you want.”

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In April, Logunov and a number of his colleagues in the lab administered the vaccine to themselves. “When you are a researcher, you are effectively going into the red zone,” he said. “You simply need to protect yourself.” He went on, “It was also thrilling to have the chance to test your technology, to see how it performs in battle.” When I spoke to Gintsburg, he told me that he had given the vaccine not only to himself and to many of his employees but also to his wife, his daughter, and his granddaughter. I asked whether he felt that he was taking a gamble. “Without excitement, it’s impossible to work, to create,” he said. “As a scientist, you should always have the desire to learn, to find things out.”

[...]

To date, more than fifty countries, including Algeria and Mexico, have preordered Sputnik V, and half a dozen plan to produce the vaccine themselves. A Phase III trial is under way in India, where a leading producer of generic medicines has already agreed to make more than a hundred million doses per year. In late December, after Argentina’s negotiations to acquire the Pfizer vaccine stalled, an Aerolíneas Argentinas jet departed from Moscow loaded with three hundred thousand doses of Sputnik V, the first of twenty-five million that Argentina has agreed to buy. In January, officials in Kyrgyzstan, concerned about the cold chain needed to transport the Pfizer vaccine, stated their preference for Sputnik V. That month, after Hungary accused the E.U. of being too slow in its vaccine rollout, the country approved Sputnik V, becoming the first in the E.U. to do so. (E.U. officials criticized Hungary for undermining European solidarity.) Such deals, Twigg pointed out, could pave the way for further diplomatic and commercial ties. “Russia could translate this reputational gain into other types of successes,” she said.

[...]

On December 2nd, the U.K. issued emergency-use authorization to the Pfizer vaccine. Not to be outdone, Putin announced the civilian rollout of Sputnik V hours later. The inoculation would begin in Moscow, with health-care workers and others who had a high risk of exposure, including teachers and social workers. A poll taken in September, however, had shown that up to half of Russian doctors and other medical professionals weren’t yet willing to get the vaccine, owing to the rushed approval process and a lack of concrete data about the safety and efficacy of Sputnik V. The Levada Center, an independent polling and research organization based in Moscow, found that, as of December, nearly sixty per cent of Russians did not wish to be vaccinated. (At the time, polls in the United States indicated that about a quarter of the population did not want to be vaccinated; in France, which has one of the largest anti-vax movements in Europe, the number hovered around fifty per cent.)

Why reopening restaurants is exactly what the coronavirus wants us to do

But epidemiologists and public health experts say a crucial factor is missing from these calculations: the threat of new viral variants. One coronavirus variant, which originated in the United Kingdom and is now spreading in the U.S., is believed to be 50% more transmissible. The more cases there are, the faster new variants can spread. Because the baseline of case counts in the U.S. is already so high — we’re still averaging about 130,000 new cases a day — and because the spread of the virus grows exponentially, cases could easily climb past the 300,000-per-day peak we reached in early January if we underestimate the variants, experts said.

Furthermore, study after study has identified indoor spaces — particularly restaurants, where consistent masking is not possible — as some of the highest-risk locations for transmission to occur. Even with distanced tables, case studies have shown that droplets can travel long distances within dining establishments, sometimes helped along by air conditioning.

Extraordinary Patient Offers Surprising Clues To Origins Of Coronavirus Variants

To be clear here, the man wasn't what doctors call a "long hauler," or a person who clears a COVID infection and then continues to have health problems for months. This man had living, growing virus in body for five months, Li says. The same infection lasted for five months.

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Every few weeks, the team extracted coronavirus from the man's body and sequenced the virus' genome.

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The sequences showed Li and his team that the virus was changing very quickly inside the man's body. The virus wasn't picking up just one or two mutations at a time. But rather, it acquired a whole cluster of more than 20 mutations.

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In other words, perhaps, the coronavirus virus uses long-term infections as a mutational testing ground. While inside one person, they can try out all these different combinations of mutations and figure out, through trial and error, which ones are best at evading the immune system or helping the virus become more infectious.

Well that sucks, not only are immuno-comprimised people more susceptible, and at a higher risk of mortality, they can potentially act as an incubator for more infectious variants.

NIT: For some reason I've become more and more annoyed when articles take to anthropomorphising the behavior of a virus. It has no intent, no desires, no objectives, no wants of any kind. The reason it continues to live and infect is because it's current structure is good at it. Any change that improves that wins by statistical advantage, not because anything or anyone "chose" the "better" version. /rant

A Missouri lawmaker sold a ‘potential cure’ for coronavirus. It was a fake stem cell treatment, feds say.

As she planned a run for the Missouri House last April, Patricia Ashton Derges went on local TV to trumpet a stem cell treatment offered at three clinics she owns as a “potential cure” for the coronavirus.

But when federal officials began investigating the claim, they found Derges was making “misleading statements” about the treatment, prosecutors said — it didn’t actually include any stem cells.

Derges, a 63-year-old Republican who was elected to the state House in November, now faces 20 criminal charges, including wire fraud and distribution by means of the Internet without a valid prescription, a federal grand jury indictment unsealed on Tuesday revealed.

A COVID-19 Testing Startup That Has Served 10 States And Congress Is Under Fire From The FDA

That debate came to a head this month when the Food and Drug Administration warned the public that the Southern California company’s tests were possibly missing coronavirus infections. This week, Curative pushed back with new data that, it claims, validates its approach.

Research done by Curative suggests that its mouth-swab test spots the virus with a high degree of accuracy in the first three weeks of an infection, including in people without symptoms, and with less accuracy for later-stage infections. That drop-off in ability is relatively unimportant during the pandemic, Curative argues, underscoring a philosophical split in testing.

The young company, and scientists who side with it, say it is most crucial to focus on catching people who are at their potentially most contagious, even if it means using a less sensitive test that may fail to pick up on people who are no longer infectious but who have lingering remnants of the virus.

Michael Mina, an epidemiologist at the Harvard T.H. Chan School of Public Health who is not involved with Curative, said the FDA appeared to be holding Curative to a nearly impossible standard of sensitivity, based on documents provided by the company. “The FDA and its deadly regulations around how they are evaluating Covid tests is inadvertently resulting in the loss of thousands of additional lives that need not be lost in this pandemic,” he said by email. “Their decision making on Curative is one example.”

Florida:

The new study only looked at data through the end of January, but the percentage of infections in Florida involving B.1.1.7 may have risen from a little less than 5 percent to approximately 10 percent in just the past week, Kristian Andersen, an immunologist at Scripps Research Institute and a co-author of the new study, said Sunday in an email.

Also Florida:

Packed bars and restaurants in Tampa tonight for Super Bowl LV

Large crowds gather in Ybor City night before Super Bowl 55 in Tampa

UK vaccine gambles paid off, while EU caution slowed it down

As with other countries that moved quickly, negotiating contracts earlier has helped Britain avoid some of the vaccine supply problems the 27-nation EU has faced — as when AstraZeneca said it hit a production issue. Valneva President Franck Grimaud told the AP that Britain will receive vaccine doses earlier because it signed first.

But the U.K. has also shown speed and agility in other areas: Its regulatory agency has authorized vaccines more quickly than the EU’s, and its government has experimented with stretching out the time between shots — allowing it to roll out first doses faster so more people can have some protection quickly.