Weekly coronavirus-related chat, questions, and minor updates - week of January 18

Usual personal update:

One of my co-teachers tested positive. We share a class in a somewhat cramped room, so this is someone who I stand six feet away from for an hour each day. We wear masks, keep the windows open, have air purifiers running, and don't go near one another, so I'm trying to tell myself that there's a chance I don't have it on account of our myriad precautions, but we share space with one another for an hour each day. We also have to project our voices through masks and over the background noise of fans, which is about the worst thing you can do for viral spread. I think it's very likely that I have it.

I already had a precautionary test scheduled for this afternoon (now that I'm back with kids and my local testing isn't swamped, I am getting myself tested twice a week), so that was lucky. I'll find out the results of that tomorrow, but it won't be definitive if it's a negative because I could still be in the incubation phase, so I'll be signing up for another test a few days from now when those appointments open. I've initiated a full quarantine already, and the next few days are going to be nerve-wracking. No symptoms yet, which is good, but that doesn't really mean anything yet given how early I likely am in the timeline.

I've been very lucky so far in all of this, but I don't know that my good luck is going to hold this time. This is by far the closest contact I've had with a positive case.

Canada’s best-kept secret? The Atlantic bubble

On the east coast of Canada, the Atlantic provinces — Nova Scotia, New Brunswick, Newfoundland and Labrador, and Prince Edward Island (PEI) — have spent the first year of the pandemic quietly honing an enviable blueprint for how to live with the coronavirus. In the region — which has a land area twice the size of the United Kingdom and a population of 2.3 million — active case numbers have mostly remained in the single or double-digits, and fewer than 100 deaths have been reported since the beginning of the pandemic. All the while, the economies haven't fared as poorly as the rest of the country.What's been dubbed the "Atlantic bubble" has been hailed as a "miracle" by some and touted as "North America's New Zealand" by others.

[...]

When the pandemic hit, public health authorities on the east coast quickly realized their health systems wouldn't be able to cope with skyrocketing cases — so they acted swiftly and strictly, imposing a set of tough restrictions, including closing parks and schools, closing the provincial borders to any non-essential travel, and mandating a two-week quarantine period for those entering the region.

Dr. Susan Kirkland, head of the epidemiology department at Halifax's Dalhousie University and a member of Nova Scotia's COVID-19 task force, says it was "one of the most successful things we've done. People who are not from the Atlantic region find that to be a very tight restriction, but quite frankly it's a tight restriction that's worked very well for us."

[...]

By July, the four Atlantic provinces were all faring so well that they formed a bubble, so residents from the four provinces could travel freely within the region without having to quarantine, while non-residents were allowed entry as long as they quarantined. The free movement within the region lasted until just before Christmas, when New Brunswick, Newfoundland and Labrador and PEI saw an uptick in cases and closed their borders — though there's already talk of re-opening the bubble.

Still going to the grocery store? With new virus variants spreading, it’s probably time to stop.

While these variants haven’t been shown to be more deadly, a more transmissible virus is actually worse in many ways than a more lethal one. Cases snowball at a faster rate, Harvard epidemiologist Marc Lipsitch said on a recent press call. With a 50 percent rise in infectiousness, for example, “in less than two weeks, you get twice the number of cases,” Lipsitch said. “And in a month or so, you have four, five times as many cases. But that’s very approximate.”

When you do have to be around other people, use a mask — but not just any mask. The other lesson of the new variants, Frieden told Vox, is that we need to get better at masking.

“The fact that [the variants] are so infectious suggests to me having a better mask is a good idea,” Frieden said. When it comes to avoiding an infection, “a surgical mask is better than a cloth mask, a tight-fitting surgical mask is better than a loose-fitting mask, and an N95 is better than a surgical mask.”

Most Americans, however, still rely on cloth masks. Part of the problem is that the CDC continues to recommend cloth masks — what should have been a stopgap measure while the government procured better, medical-grade masks for citizens, Zeynep Tufekci and Jeremy Howard pointed out in the Atlantic.

I've been going to the grocery store once or twice a week pretty consistently, because (at least here in Seattle) everyone is good about wearing masks and social distancing in the store. Going to re-think that now.

Why Aren’t We Wearing Better Masks?

Tragically, America is swamped with fraudulent medical-grade masks, some of which are only 1 percent effective. Many masks do not have labels clearly indicating their manufacturer. Some official mask-testing methods are inappropriate, including the use of far higher pressure than normal breathing exerts. No reasonable certification is available for the most useful masks generally available to the public. All of this means that everyone has to somehow figure out for themselves which masks are effective.

We routinely get PR pitches for excellent new solutions as well as snake-oil remedies, and we sometimes have trouble telling them apart—how is an ordinary person supposed to evaluate competing claims? When we share our articles about masks on social media, we are asked where to buy proper masks. Not only do we have no answer, but we often find that marketers will answer instead, directing readers to unreliable, overpriced masks. Worse, the supply situation apparently remains so dire that the CDC still “does not recommend that the general public wear N95 respirators,” because they’re crucial supplies that must continue to be reserved for health-care workers and other first responders.

Not all countries have this problem. Taiwan massively scaled up its manufacturing of masks at the start of 2020, such that by April every citizen received a fresh supply of high-quality masks each week, and the distribution system was regulated by the government. Taiwan’s COVID-19 death rate per capita is more than 1,000 times lower than that in the U.S. Hong Kong has been distributing patented six-layer masks (the efficacy of which has been laboratory tested) to every citizen. Singapore is on at least its fourth round of distributing free, reusable, multilayer masks with filters to everyone—even kids, who get kid-size ones. In Germany, Bavaria has just announced that it will be requiring higher-grade masks. If all of these places can do this, why can’t we?

Fixing this problem is more urgent now that a new variant of the coronavirus, known as the B.1.1.7 lineage, is making its way around the world. [...]

I don’t know what to buy either but I think it’s long past time to try actual N95 masks and ordered these based on a review.

A Black American woman who moved to Bali, Indonesia, last year is facing deportation and intense backlash after promoting the sale of an e-book she wrote with her girlfriend to help others move to the country during the pandemic.

"In March, when the pandemic hit and our 6-month plan went out the window, we decided to stay in Bali to 'wait it out' and we've been here ever since," Gray wrote, adding a list of "major benefits of moving to Bali" that included "Luxury Lifestyle" and "Queer Friendly."

Their e-book, which sold for $30, included "direct links to our visa agents and how to get into Indonesia during COVID," she wrote.

The thread sparked massive outrage among Indonesians and the wider Southeast Asian community. They said Gray was encouraging an influx of Westerners to travel to a country that has closed its borders to foreigners over the worsening COVID-19 situation.

It's a refreshing change of pace, I guess, to have an example of "don't brag about doing crimes on social media" that doesn't involve the US Capitol insurrection.

Biden signs order requiring masks on planes, buses, trains and at airports

Biden’s move marks a clear break from Trump’s handling of masks, although some specifics, including how it might be enforced, remain unclear pending the release of the order. It will require masks “on certain public modes of transportation and at ports of entry to the United States,” according to a White House strategy document released Thursday.

Why scientists are more worried about the Covid-19 variant discovered in South Africa

There’s evidence from several small, and not-yet-peer-reviewed, studies that mutations in the South Africa variant — known as 501Y.V2 and already present in at least 23 countries — may have a higher risk of Covid-19 reinfection in people who’ve already been sick and still should have some immunity to the disease.

Scientists haven’t confirmed that this variant is more contagious, though evidence is pointing in this direction. They’re also concerned that 501Y.V2 could have implications for treatments for Covid-19. Regeneron, a company that has developed a cocktail of two monoclonal antibodies as a therapy for patients with the illness, reported that 501Y.V2 may be able to evade one of the antibodies in its mix. The drug is still effective, but subsequent mutations could render it less so.

But perhaps most alarming is the prospect that the mutations in the variant could limit the effectiveness of existing vaccines, one of the best tools we have for controlling the pandemic.

The results of these recent studies are “a serious indication we have to look hard at how well vaccines might work,” Penny Moore, a virologist at the National Institute for Communicable Diseases in South Africa, told Vox. Taken together, they highlight the dangers of letting Covid-19 spread unchecked and also portend the challenges that lie ahead as the virus continues to evolve.

In 21 cases — nearly half — the existing antibodies were powerless against the new variant when exposed in test tubes. This was especially true for plasma from people who had a mild previous infection, and lower levels of antibodies, to begin with.

The findings suggest immunity from previous versions of the virus might not help individuals fend off the new variant if they’re exposed, particularly if their prior case was mild or symptom-free.

Biden’s Covid-19 Plan Is Maddeningly Obvious

In short, the article argues, this administration's failure to contain the coronavirus can be traced to a lacking federal response. Ultimately a pandemic is an international problem; but instead of acting in concert with other nations, the Trump admin abdicated its responsibility to lead at any level, leaving us with haphazard state-level responses as though viruses respect state borders. Even worse, due to the lack of coordination, states were forced to compete against each other for resources.

Even Operation Warp Speed, perhaps the only federal response approaching a semblance of success, is still marred by failures. Vaccines have now been developed -- a fact that would hold true even without Operation Warp Speed -- but the distribution infrastructure does not exist, leaving the US tens of millions of vaccinations short when compared to past projections.

Long read in Politico: The crash landing of 'Operation Warp Speed': Born as a second Manhattan Project, the Trump administration vaccine program actually achieved most of its goals – until distribution problems marred its success.

Complete with HHS secretary Alex Azar going full Michael Scott about the distribution failures:

And asked if he was disappointed by recent news of setbacks, the cabinet secretary who steered the project offered a response as enigmatic as the program itself.

“You fail to achieve 100 percent of the goals you do not set," Azar says now.

On the lighter side of things:

Man Allegedly Hid From Coronavirus And Authorities In Chicago Airport For 3 Months

Honestly, I'm impressed. I hope he writes a memoir.

Single Covid vaccine dose in Israel 'less effective than we thought'

Israel’s coronavirus tsar has warned that a single dose of the Pfizer/BioNTech vaccine may be providing less protection than originally hoped, as the country reported a record 10,000 new Covid infections on Monday.

Questions over the effectiveness of the vaccine were raised amid reports that thousands of Israelis were still becoming sick after receiving the vaccine, although the public health services head, Sharon Alroy-Preis, said that in most cases this was because the individuals had not built up sufficient antibodies after being inoculated before being exposed to the virus.

Difficult to untangle how much of this is a single dose not providing as much protection vs. people taking more risks as soon as they get the first dose rather than waiting for immunity to develop.

Amid warnings that 30% to 40% of the new infections were being driven by a Covid-19 variant first identified in the UK, the Israeli cabinet was meeting on Tuesday to consider tightening existing restrictions. Some analysts, however, have put the prevalence of the new variant at lower levels.

...plus, of course, the additional variable that the more-transmissible UK variant may not be deterred by a single vaccine dose.

America’s Most Reliable Pandemic Data Are Now at Risk

Since July, [hospital] data have been routed through the Department of Health and Human Services, but some officials inside the CDC are trying to regain control. It might seem obvious that the CDC, the traditional repository of infectious-disease information, should win this intragovernmental battle, but the reality is much more complicated. The current, HHS-run system works—unlike so much else in the response—and with these data flowing in, the federal government can dispatch help to hospitals that need it. If the new administration changed that system, it would be setting aside the best available data about the pandemic, and gambling that it could build a better system when it cannot afford to lose.

[...]

At the COVID Tracking Project, we were initially dismayed by the HHS changeover, but we watched closely as the system stabilized and began to become more reliable. In a series of analyses that we ran over the past several months, we came to nearly the opposite conclusion of other media outlets. The hospitalization data coming out of HHS are now the best and most granular publicly available data on the pandemic. This information has changed the response to the pandemic for the better.

[...]

The idea that the Trump administration would try to suppress COVID-19 data was not far-fetched, but the HHS staffers I spoke with said that public perception was misguided. The people on the team were not Trump-administration loyalists, but civil servants from across the federal government. Its leader, Amy Gleason, came from the U.S. Digital Service, a signature achievement of the Obama administration that brings technologists into the government from private industry.

The headline is alarmist and the article seems somewhat disorganized, but it seems they're happy with the HHS hospital data.

Tweet thread from Trevor Bedford, my virology whisperer

Important new study by Wibmer et al (https://biorxiv.org/content/10.1101/2021.01.18.427166v1) of neutralization by convalescent sera on wildtype vs 501Y.V2 variant viruses circulating in South Africa. It shows that mutations present in 501Y.V2 result in reduced neutralization capacity.

I don't claim to understand the details, but here's his summary:

However, if these results are confirmed by further studies, my guess based on the seasonal influenza comparison is that we need to investigate the manufacturing timeline and regulatory steps required to update the "strain" used in the vaccine.

501Y.V2 is still largely restricted to South Africa, but it (or other antigenically drifted variants) may spread more widely in the coming months. I would be planning this potential "strain" update for fall 2021.

And all this said, I'll be getting the vaccine as soon as I'm able. We have an amazing vaccine now that works against currently circulating viruses. And if it becomes necessary, this emerging situation can be dealt with through a forthcoming vaccine update.

Grocers Have A Strategy To Get Their Workers Vaccinated Against COVID-19: Pay Them

Covid: Brazil approves and rolls out AstraZeneca and Sinovac vaccines

A nurse has received Brazil's first Covid-19 vaccine dose after regulators gave emergency approval to two jabs.

Brazilian state regulator Anvisa gave the green light to vaccines from Oxford-AstraZeneca and China's Sinovac, doses of which will be distributed among all 27 states.

(P.S: It's 26 states and the federal district AKA the capital. Rookie mistake.)

Health Minister Eduardo Pazuello told reporters that the national vaccination programme in the country of 211 million people would begin in earnest in the coming days. Two Brazilian biomedical centres which have been given approval to produce the jabs will be heavily involved.

About six million doses of the Sinovac-developed CoronaVac have already been produced in Brazil, while the government is waiting for shipments of the AstraZeneca vaccine from a laboratory in India.

A brief opinion piece from a Brazilian:

This has been a rare piece of good news today for Brazilians who are grappling with a devastating second wave.

From where I am, the city of Manaus, the vaccine does not feel real. People here are trying to recover a collapsed health system and doing what they can to keep their sick relatives alive.

Earlier this week researchers said the Chinese vaccine had been found to be 50.4% effective in Brazilian clinical trials. This, results showed, was significantly less effective than previous data suggested - barely over the 50% needed for regulatory approval.

The news comes after revelations that a new coronavirus variant has emerged in Brazil. Several cases were traced back to the Amazonas state, where a state of emergency is in place.

Looks like there's a new website for finding the vaccine in Massachusetts. It seems to be pretty rough and they're going to redo it.

A pretty detailed blog post, though speculative in parts.

Exploring the Supply Chain of the Pfizer/BioNTech and Moderna COVID-19 vaccines

Both Pfizer-BioNTech and Moderna each have two largely independent supply chains in Europe and the United States. This makes sense in order to maximize utilization of available manufacturing capacity and to add resilience through redundancy. Bloomberg’s Supply Lines newsletter points out that it also appeases certain “protectionist governments intent on hobbling international cooperation by exerting sovereignty over supply chains”.

[...]

Pfizer owns marketing and distribution rights for all but three countries in the world. Those three exceptions are: Germany and Turkey where BioNTech themselves markets and distributes, and China where Shanghai Fosun Pharma holds the marketing rights.

[...]

Pfizer intends to bypass government-operated distribution processes in all countries. [...] This is well-aligned with Pfizer’s stated goal to start selling the vaccine to customers other than governments in the future.

In the United States the government supplies these supplies, as part of Operation Warp Speed (OWS). Kitting and delivery of Moderna and all future OWS partners’ kits is handled by OWS distribution partner McKesson.69 In this system, Moderna vaccine shipments are accompanied by the supplies required to administer them. As usual, Pfizer bypasses the government-operated supply chain and ships “mega kits” of supplies that contain enough materials to administer 1,000 doses as well as one set of gloves for handling dry ice. “Mega kits” arrive at the point of care separately from the vaccine.

So, it seems that confusion about vaccine supplies might in part be due to which vaccine you're talking about? Pfizer does everything themselves while Moderna works with the government.

New head of the Ohio state senate's health committee seems like a nice dude

A Republican lawmaker and doctor who questioned whether members of “the colored population” were disproportionately contracting the coronavirus because of their hygiene is drawing new criticism from Black lawmakers after his appointment to lead the state Senate Health Committee.

“Could it just be that African Americans – or the colored population — do not wash their hands as well as other groups? Or wear masks? Or do not socially distance themselves?” state Sen. Stephen Huffman asked a Black health expert in June 11 testimony. “Could that just be the explanation of why there’s a higher incidence?”

Huffman, of Tipp City, was appointed last week by Senate President Matt Huffman, his cousin, to chair the committee even after he was fired from his job as a Dayton-area emergency room physician for his comments.

New Zealand Records 1st Suspected COVID-19 Community Case Since November

A 56-year-old woman, who had traveled to Spain and the Netherlands for work late last year, has tested positive for the coronavirus after being in managed isolation for the required 14 days upon her return to New Zealand, the country's Ministry of Health said.