Weekly coronavirus-related chat, questions, and minor updates - week of December 21

Usual personal update:

Here’s the score, heading into my winter break:

• We've had over 40 confirmed cases (cumulatively) in the specific school building in which I work.
• One school in my district had to go fully remote due to too many staff out and no substitutes to fill their positions.
• Local percent positivity is alarmingly high (well over 5%), and testing capacity is far below demand.

I’d love to give more data and more precise numbers but don’t want to offer up identifying information about myself. Suffice it to say that nearly any data point I could offer right now would be as bad as, if not worse than, it’s ever been. If we’re measuring where we’re at using the standard stoplight green-yellow-red scale, we hit alarm-level red a long time ago and have since been trending towards the brightest, deepest red one can possibly envision.

My last exposure to others is today, but yesterday and today have seen so many absences at school that I actually feel far safer than normal because I’m sharing space with far less people than normal.

I’ve been refreshing my local COVID testing appointment scheduler constantly and was able to book an opening for this coming Saturday. I made the appointment yesterday, and it was the first available slot, which says something about testing throughput (which is further exacerbated by holiday closures). Saturday will be 4 days after my last exposure, which isn’t great, but honestly for me it’s more about accumulated exposures. It's 5 days from Monday, 8 from the prior Friday, and so on. A negative test won’t tell me I’m safe from this Tuesday, but it will almost definitively tell me whether I’m safe from Monday through Friday of last week, which is where my real worry lies.

One huge benefit of teaching is time off, so I get the luxury of having almost two full weeks away from work for the holidays. This is usually a time of togetherness for me personally, and I know a lot of others are struggling with whether or not it’s safe to see their families, but I’m going to be honest: during these next two weeks I want nothing more than to not have to come into in-person contact with any other human being save for my husband (and that’s exactly what I’m going to do). If I test negative on Saturday and have no symptoms, I will be able to take the next week “off” from personal COVID worries and spend time with my husband in our own home without worrying I might infect him — something I haven’t been able to do since September.

I’m not in the clear yet, and I’m trying not to get my hopes up, but it’s going to feel amazing leaving school today with the knowledge that I don’t have to put myself at any additional risk, other than what I've already been exposed to, for nearly two weeks. No symptoms and a negative test on the 26th will be the greatest Christmas gift I could ever possibly get.

Despite what I’m facing, I realize I’m actually lucky compared to many others out there. I’m not a healthcare worker, nor have I lost my job or a loved one. As the pandemic has dragged on and I see the darker effects of COVID in those I know and come into contact with, like my students’ families, I can see clearly all the things I shouldn’t take for granted and all the hurt and burdens that others are unfairly living with. For all those in worse situations, my heart goes out to you.

There appeared 2 new mutated versions of Corona (1 in England, 1 in South Africa)

The one in England has 16 mutations (which is very much in such a short time) and is already responsible for 60% of the corona infections in London.
They don't know much about it yet, but it is expected to spread much more easily than the original strang. Otherwise, it seems to stay close to the original and they are hopeful that the vaccine still works.

In response to that other countries (e.g. wales, germany, france) locked down their airports.

This brings out the fear of the virus again and what this could mean for the new year

Edit: There are already cases with the english mutation reported in some european countries

The US Congress appears to have (FINALLY) settled on what's going into their next COVID relief bill : https://www.npr.org/2020/12/21/948744901/here-is-whats-in-congress-covid-19-relief-package

It only took them most of the goddamn year.

Personal update: my office switched back to essential personnel only yesterday. They had allowed an additional 20 staffers to start coming back on-site in September, working on staggered schedules and with strict masking and social distancing protocols. But the metrics have gotten too high in NYC, so we're paring back to the skeleton crew. I'm now the only person working on my floor again, with a handful of other engineers working one floor down. Everyone else works from home. (Our company has about 300 employees, only about a dozen of us are allowed in the building.)

This week is significant as it truly marks the beginning of the end of the pandemic. It's very nice to finally have a chart of growing numbers that is actually good news: Vaccination counts.

I'm still months away from getting vaccinated, but psychologically it's very nice to see progress now.

A more personal rant below. I'm completely out of patience for the more overbearing measures that are currently being applied in Belgium, and so is a lot of the country. There's complaints that the third wave may mean an extra month of lockdown, which would take us all the way to mid-february before we're out of lockdown, which is absolutely fucking bonkers.

At this point, a lot of people have stopped respecting the rules altogether. Let's dig down into why.

This is the problem with overbearing rules: If you are too strict on the stuff that matters less, people will stop respecting those that matter more. Even the easy ones.

Rules need to be optimized for highest impact against the virus with lowest impact across the population.

Lowest hanging fruit is of course the mask mandate. Masks have already been distributed, so the hard part of it is done. They're easy to wear and a mild annoyance that people can put up with due to the situation.

Another fairly low hanging fruit is reducing crowd densities. This is less easy as there's a variety of ways to do it, and it can decrease revenue for some businesses. But it's an easy one to live with temporarily.

The third low hanging fruit that isn't being applied at all right now is air filtration requirements for indoor spaces. We've seen how much of an impact this has on the virus. It is hard to implement but, fuck, I'm sure a lot of businesses out there would prefer implementing air filtration than being forced to close. This includes schools: If you insist on keeping schools open (you shouldn't… but whatever), then at least reduce their impact.

Instead, what do we have?

Belgium’s Covid Christmas rules: Only one guest can use the toilet

Fuck off. This is how you lose people's will to put up with the rules.

From a blog post by Bill Gates about new COVID-related technology to expect in 2021:

How do you make 5 to 10 billion doses?

The world will have to manufacture around 5 billion doses if there’s a vaccine that requires only one dose, or 10 billion in the current scenario of two-dose vaccines. (This is assuming that 70 percent of the global population must be covered in order to break transmission of the disease.)

Is 5 to 10 billion doses a lot? Well, all the vaccine companies in the world typically produce a total of fewer than 6 billion doses a year. That includes flu shots, routine childhood immunizations, and so on. So to produce all the COVID-19 vaccines needed without cutting back on any others, the manufacturing capacity will at least need to almost double, and more likely almost triple.

To help ease the manufacturing burden, our foundation helped put together what’s called “second-source agreements.” We paired vaccine companies in rich countries with counterparts in developing countries that specialize in producing safe, high-quality, and affordable doses at a very high volume.

A second-source agreement is designed to make the most of both skill sets. A company that excels at production agrees to manufacture products designed by another company with a viable vaccine candidate. For example, the biggest vaccine manufacturer in the world, Serum Institute of India, is producing doses of AstraZeneca’s vaccine. They’ve already begun production, so there will be doses available for low- and middle-income countries if AZ’s vaccine is approved for use. And our foundation took on some of the financial risk, so if it doesn’t get approved, Serum won’t have to take a full loss.

It’s hard to overstate how unusual these second-source agreements are. Imagine Ford offering up one of its factories for Honda to build Accords. But given the scale of the problem and the urgency of solving it, many pharmaceutical companies are seeing the benefit of working together in new ways like this.

[...]

Another approach to treatment you may have read about is called monoclonal antibodies. These are created by taking the antibodies in the blood of COVID-19 survivors and flowing them past a spike protein to see which ones stick the most. (The stickier they are, the better they are at attacking the virus.) Then you figure out the gene sequence that makes that antibody, use a factory to make billions of copies of it, and give them to patients.

Although you may not have heard about antibody treatments before the pandemic, there’s nothing new about them. Today they’re used in some of the most popular medicines in the world, including arthritis treatments.

The key question surrounding COVID-19 antibodies is whether manufacturers make enough of them so they can be delivered to the entire world? It depends partly on the size of the required dose. Some treatments have involved doses as large as 8 grams. If something substantially smaller—such as 0.5 grams—works well, then it will be possible to treat far more people. Scientists also need to see if it’s possible to replace the current IV infusion with a two-shot dose.

If researchers solve the dosage and infusion challenges, then the main limiting factor will be manufacturing capacity. To deal with that, our foundation underwrote a second-source agreement in which Fujifilm Diosynth will produce an antibody developed by Eli Lilly. These doses will be earmarked for low- and middle-income countries and priced accordingly, so that millions of affordable doses will be available within 90 days of regulatory approval.

[...]

Several companies are working on rapid tests that could be produced by the tens of millions. One is the British company LumiraDx, which has created a device that’s roughly the size of a thick cell phone, with a card reader at one end. A health care worker takes a sample from a patient, inserts it into the machine, and gets results within 15 minutes. After removing any personal information that could identify the patient, the device uploads the results to a central server. Analysts then use the data to follow the disease in real time, giving policymakers up-to-the-minute information on where to focus prevention and treatment efforts.

Our foundation is part of an effort to deploy an initial supply of 5,000 readers in 55 countries throughout Africa. Although that’s a relatively small number for such a large area, it’s a good start. And the benefits may not be limited to COVID-19: In the future, the same machines could be used to test for HIV, tuberculosis, and other diseases.

Still other companies are working on ways to make the highly sensitive tests that are in use now faster and cheaper, and to expand the manufacturing of less-sensitive but cheaper tests from tens of thousands a day to many millions a day.

https://tinyurl.com/FAQ-aerosols

The goal of these FAQs is to provide information to the general public in an efficient manner about how to prevent aerosol transmission of COVID-19, with the hope that this will allow more informed decision making by individuals or organizations.

A well cited resource for the science behind, risks, and prevention measures for aerosol transmission put together by a well credentialed panel.

Five of us were speakers at the recent Workshop on Airborne Transmission of COVID-19, organized by the US National Academies of Sciences, Engineering, and Medicine (the highest level scientific organization in the US). Three of us are members of a COVID-19 WHO expert group.

Aerosol transmission is something I hadn't heard CDC or the WHO address (the authors address why in the document). I've felt uncomfortable being near anyone unmasked, and been uneasy encountering mouth only maskers in stores - even though I was able to maintain 6-10 feet of distance. This document indicates that unease was well founded. As more and more research indicates that transmission isn't only from direct close physical contact, we as a society will need to update our strategy. It's about 60 pages with figures but is a pretty quick read.

The TSA screened 1.2 million people at airports in the US yesterday, the highest single-day total since March 16. So there are definitely a lot of people still flying (and almost certainly to attend gatherings).

US hospitals facing worrisome shortage of nurses, doctors

California, which is enduring by far its worst spike in cases and hospitalizations, is reaching out to places like Australia and Taiwan to fill the need for 3,000 temporary medical workers, particularly nurses trained in critical care.

[...]

Hospitals in some states have enlisted retired nurses and students. In Alabama, more than 120 students and faculty members from the University of Alabama at Birmingham’s nursing school began helping with care last week at UAB Hospital.

[...]

South Carolina Gov. Henry McMaster tested positive for the virus and was to receive outpatient antibody treatment for “mild symptoms,” his office said Tuesday.

In Tennessee, which is seeing the nation’s worst new COVID-19 infection surge per capita, the state health commissioner has warned that combining the Thanksgiving surge with another would “completely break our hospitals.”

Deaths in Florida’s nursing homes doubled during the Thanksgiving holiday, according to statistics gathered by AARP. The rise drew concern from advocates also worried about gatherings over Christmas and other year-end celebrations.

[...]

An emergency room physician in Los Angeles who helped set up a surge hospital last spring said there are no plans to reopen it. “There would be no way to staff it,” said Dr. Marc Futernick.

[...]

Dr. Mark Ghaly, California’s Health and Human Services secretary, said the state is “lucky to get two-thirds” of its requests for travel nurses fulfilled right now.

[...]

Ghaly said entire areas of California may run out of room even in surge capacity units “by the end of the month and early in January.” It’s trying to avoid that by opening makeshift hospitals in places like gymnasiums, tents and a vacant NBA arena, and sending patients to parts of the state with empty beds.

On the (slightly) lighter side, the latest comic in the children's series Priya : https://www.npr.org/sections/goatsandsoda/2020/12/21/945039159/indias-female-superhero-and-her-flying-tiger-are-out-to-fight-the-pandemic

Then Priya hops across the border to Pakistan where she teams up with another iconic South Asian female superhero: Jiya from Pakistan's comic series Burka Avenger. Together, they tackle the mustachioed (and unmasked) Baba Kaboom, who wants to spread the virus all over the town of Chutneyville.

Devineni had long wanted to connect Jiya and Priya, and the virus gave him that opportunity. "The virus doesn't respect borders," says Devineni. "I thought we could come together to fight the epidemic."

COVID-19 Strikes Antarctica As Chilean Base Hit With Virus

A total of 36 people stationed at Chile's General Bernardo O'Higgins Riquelme research base in Antarctica, including 26 members of the Chilean Army and 10 civilian maintenance contractors, recently tested positive for COVID-19, according to multiple Spanish-language reports on Monday.

[...]

At least some of the infected individuals were said to have experienced symptoms before testing positive for the virus, according to the Associated Press. All 36 have since been evacuated to the city of Punta Arenas in Southern Chile, where they are reported to be under isolation and in good condition. The station personnel were replaced by a new crew who had been quarantined and tested negative prior to their journey.

1 person went to work sick; ensuing outbreak killed 7 in Douglas County, Oregon

Earlier this month in Douglas County, one person who was sick went to work, and later tested positive for the coronavirus.

Within two weeks, that one action led to two subsequent outbreaks. The first killed at least seven people, nearly 20% of the county’s total COVID fatalities since the pandemic began. The second forced more than 300 people into quarantine.

Coronavirus live updates: Over half of California ICU patients infected with virus, capacity slips to 1.1%

Bay Area ICU capacity drops to lowest yet: The Bay Area’s available intensive care capacity in hospitals has tightened again, slipping to 11.4% on Wednesday, down from the 13.5% where it had hovered for a couple of days. The new data from California health officials show the state’s most stretched regions, San Joaquin Valley and Southern California remaining at 0% ICU capacity, while the greater Sacramento region dipped again, to 15.6%. Northern California, the only region that is not under mandatory state shutdown restrictions, had 28.8% ICU capacity left.

[...]

Santa Clara County hospitals “on the brink”: Only 35 intensive care unit beds are available in all of Santa Clara County, officials said Wednesday, and 8 out of 10 hospitals have fewer than five beds available. More than 68 patients are waiting for beds, and hospitals are at a breaking point, said Dr. Ahmad Kamal, the county’s COVID-19 director of health care preparedness, “On the other side of that line are things that would have been unthinkable,” he said. “We are talking about people in gurneys without a bed to get into. ... We are talking bout people dying who should not have died.”

[...]

Nearly half of Kaiser hospitals out of ICU capacity in California: Kaiser Permanente, one of the state’s largest health care providers, has run out of ICU capacity in 16 of its 36 hospitals statewide, Kaiser CEO Greg Adams said Tuesday. “Today we’re over 100% of our usual patient volume, and of that volume, 52% of our inpatients are patients diagnosed with COVID,” he said. “Sixteen of our 36 hospitals are already above 100% occupancy in our ICUs. We’re struggling to add capacity for COVID patients as we speak.”

Japan to halt new entry of foreign nationals over new virus strain

(insert Madagascar joke here)

Japan will temporarily suspend new entry into the country of nonresident foreign nationals from around the world from Monday through the end of January as a precautionary step against the new, potentially more transmissible coronavirus variant, the government said Saturday.

The news came the same day Japan confirmed two more people to have been infected with the new variant, following its first cases of the strain detected in five people the previous day.

With Few Takers for COVID Vaccine, DC Hospital CEO Takes ‘One for the Team’

[Howard University Hospital], located on the campus of one the nation’s oldest historically Black colleges, received 725 doses of the vaccine made by Pfizer and BioNTech on Dec. 14 and expects 1,000 more vaccine doses this week to immunize its workers.

Yet, as of Friday afternoon, about 600 employees had signed up for the shots, touted as about 95% effective in preventing the deadly disease. Howard has about 1,900 employees, not counting hundreds of independent contractors it also hoped to vaccinate.

[...]

Howard, which has treated hundreds of COVID patients, was one of six hospitals in the city to get the first batch of nearly 7,000 doses of the Pfizer vaccine Monday. About one-third of those doses were administered by Friday morning, said Justin Palmer, a vice president of the District of Columbia Hospital Association.

US deaths in 2020 top 3 million, by far most ever counted

Final mortality data for this year will not be available for months. But preliminary numbers suggest that the United States is on track to see more than 3.2 million deaths this year, or at least 400,000 more than in 2019.

U.S. deaths increase most years, so some annual rise in fatalities is expected. But the 2020 numbers amount to a jump of about 15%, and could go higher once all the deaths from this month are counted.

[...]

A burst of pneumonia cases early this year may have been COVID-19 deaths that simply weren’t recognized as such early in the epidemic. But there also have been an unexpected number of deaths from certain types of heart and circulatory diseases, diabetes and dementia, Anderson said.

Many of those, too, may be related to COVID. The virus could have weakened patients already struggling with those conditions, or could have diminished the care they were getting, he said.

[...]

Data for all of 2020 is not yet available. But last week the CDC reported more than 81,000 drug overdose deaths in the 12 months ending in May, making it the highest number ever recorded in a one-year period.

Experts think the pandemic’s disruption to in-person treatment and recovery services may have been a factor. People also are more likely to be taking drugs alone — without the benefit of a friend or family member who can call 911 or administer overdose-reversing medication.

But perhaps a bigger factor are the drugs themselves: COVID-19 caused supply problems for dealers, so they are increasingly mixing cheap and deadly fentanyl into heroin, cocaine and methamphetamine, experts said.

Should pregnant women get the COVID-19 vaccine? Will it protect against asymptomatic infections and mutated viruses? An immunologist answers 3 questions

Can I get vaccinated if I am pregnant or breastfeeding?

Yes, you can and should get a COVID-19 vaccine if you are either pregnant or breastfeeding.

Will I be protected from asymptomatic infection?

Initial data shows 60% protection from asymptomatic infection after the first dose of the Moderna mRNA vaccine. It is likely Pfizer will also protect from asymptomatic infection, but this has not yet been shown. This means that your risk of getting an asymptomatic infection is reduced by more than half after the first dose of the Moderna vaccine.

Will new versions of the SARS-CoV-2 virus succumb to the vaccine?

Fortunately all of the versions of the SARS-CoV-2 virus identified to date are neutralized by the COVID-19 vaccines.