Lunchtime Pandemic Reading, 15-January-2021
2 million dead
Lunchtime pandemic reading.
Standard disclaimer: this is a roundup of informative pieces I've read that interest me on the severity of the crisis and how to manage it. I am not a qualified medical expert in ANY sense; at best I am reasonably well-read laity. ALWAYS prioritize advice from qualified healthcare experts over some person on Facebook.
This is also available as an email newsletter at https://lunchtimepandemic.substack.com if you prefer the update in your inbox.
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The world just crossed 2 million deaths from COVID-19. Within days, the United States will lead that with 400,000 dead. Within a week or so, we will hit 100 million cumulative cases.
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The United States has exhausted its vaccine reserve. "When Health and Human Services Secretary Alex Azar announced this week that the federal government would begin releasing coronavirus vaccine doses held in reserve for second shots, no such reserve existed, according to state and federal officials briefed on distribution plans. The Trump administration had already begun shipping out what was available beginning at the end of December, taking second doses directly off the manufacturing line.
Now, health officials across the country who had anticipated their extremely limited vaccine supply as much as doubling beginning next week are confronting the reality that their allocations will not immediately increase, dashing hopes of dramatically expanding access for millions of elderly people and those with high-risk medical conditions. Health officials in some cities and states were informed in recent days about the reality of the situation, while others are still in the dark.
Because both of the vaccines authorized for emergency use in the United States are two-dose regimens, the Trump administration’s initial policy was to hold back second doses to protect against the possibility of manufacturing disruptions. But that approach shifted in recent weeks, according to the officials, who spoke on the condition of anonymity because they were not authorized to discuss the matter. The result is that next week’s allocations will remain flat.
These officials were told that Operation Warp Speed, the Trump administration’s initiative to speed the development of vaccines and therapeutics, stopped stockpiling second doses of the Pfizer-BioNTech vaccine at the end of last year, instead taking second doses directly off the manufacturing line. The last shots held in reserve of Moderna’s supply, meanwhile, began shipping out over the weekend."
Source: https://www.washingtonpost.com/health/2021/01/15/trump-vaccine-reserve-used-up/
Commentary: I am unsurprised by this revelation. If a new strain evolves to counter the vaccines, it will be in the United States where our rollout is haphazard at best.
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Use of AI to predict mutation. "Viral mutations that evade neutralizing antibodies, an occurrence known as viral escape, can occur and may impede the development of vaccines. To predict which mutations may lead to viral escape, Hie et al. used a machine learning technique for natural language processing with two components: grammar (or syntax) and meaning (or semantics) (see the Perspective by Kim and Przytycka). Three different unsupervised language models were constructed for influenza A hemagglutinin, HIV-1 envelope glycoprotein, and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike glycoprotein. Semantic landscapes for these viruses predicted viral escape mutations that produce sequences that are syntactically and/or grammatically correct but effectively different in semantics and thus able to evade the immune system.
The ability for viruses to mutate and evade the human immune system and cause infection, called viral escape, remains an obstacle to antiviral and vaccine development. Understanding the complex rules that govern escape could inform therapeutic design. We modeled viral escape with machine learning algorithms originally developed for human natural language. We identified escape mutations as those that preserve viral infectivity but cause a virus to look different to the immune system, akin to word changes that preserve a sentence’s grammaticality but change its meaning. With this approach, language models of influenza hemagglutinin, HIV-1 envelope glycoprotein (HIV Env), and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Spike viral proteins can accurately predict structural escape patterns using sequence data alone. Our study represents a promising conceptual bridge between natural language and viral evolution."
Source: https://science.sciencemag.org/content/371/6526/284
Commentary: This is a logical and insanely cool application of natural language processing. Viral RNA does have to follow rules for the virus to be viable, just as language has to follow rules to be understandable. Training an AI to recognize viral rules helps rule out mutations that make no sense. This could drastically speed up vaccine adaptation to new mutations by ruling out or even preparing in advance for logical mutations of a virus. So cool.
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Vox advocating for less store time. "Recent developments in the Covid-19 pandemic have exposed a grim reality: If we keep doing what we’re doing now to prevent infections, we’re screwed. Well, even more screwed.
That’s because the virus appears to be getting even better at infecting us. Since at least December, new, more contagious variants of the SARS-CoV-2 virus that causes Covid-19 have been outcompeting earlier versions of the virus in countries as far and wide as Brazil, the UK, and South Africa.
The advantage the new variants carry seems to be that in any given situation where people are gathered, they’ll infect more people — an estimated 30 to 70 percent more in the case of the B.1.1.7 variant first identified in Britain, which has now been identified in 50 countries.
The implication is clear: If we want the pandemic to end as fast as possible, we need to pump the brakes right now. And we don’t have to wait for the vaccines to slow the spread of the virus. We simply need to do what we’ve been doing all along to prevent infections, just much, much better. At an individual level, that means avoiding optional gatherings with other people — even grocery trips — whenever possible, or cutting them very short.
“Shopping for five minutes in the grocery store is a lot better — six times better — than shopping for 30 minutes,” said Tom Frieden, the former director of the Centers for Disease Control and Prevention, since the odds of becoming infected rise the longer you’re exposed. “Picking up groceries at the curbside is even better, and having them delivered is even better still.” (If you’re able to get groceries delivered or pick up curbside, it will also help reduce the risk for those who can’t.)
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.”"
Source: https://www.vox.com/22220301/covid-spread-new-strain-variants-safe-grocery-store-n95-masks-vaccine
Commentary: We've been saying for a while to wear the best mask available to you in high risk places. With these new strains, any indoors place is a high risk place. Wear N95 or better masks - N100/P100 are the very best, and offer sufficient protection that the odds of a virus sneaking through - as long as your filters are sterilized regularly and your mask is properly fitted - are very low.
Here's an easy test: you know what dust and dirt smells like, and it probably makes you sneeze. Put your mask on, then find a place in your home with a lot of dust, like under your bed. Using some kind of air blower - the output of a vacuum cleaner, a vigorously swept broom, an air mattress pump, etc. - blow a crap ton of dust in the air. If you can smell it, if it makes you sneeze, then your mask is insufficient. If you can't smell anything, and the dust doesn't bother your nose and mouth (you might want goggles on when doing this) then your mask is stopping particles.
Avoid indoor places. Wear the best mask available to you.
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A reminder of the simple daily habits we should all be taking.
1. Always wear the best mask available to you when out of your home and you'll be around other people. Respirators are back in stock at online retailers, too.
2. Get vaccinated as soon as you're able to.
3. Wash/sanitize your hands every time you are in or out of your home for any reason.
4. Stay home as much as possible. Minimize your contact with others and maintain physical distance of at LEAST 6 feet / 2 meters, preferably more. Avoid indoor places as much as you can; indoor spaces spread the disease through aerosols and distance is less effective at mitigating your risks.
5. Get your personal finances in order now. Cut all unnecessary costs.
6. Replenish your supplies as you use them. Avoid reducing your stores to pre-pandemic levels in case an outbreak causes unexpected supply chain disruptions.
7. Ventilate your home as frequently as weather and circumstances permit, except when you share close airspaces with other residences (like a window less than a meter away from a neighboring window).
8. How to properly fit a mask:
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Common misinformation debunked!
There is no mercury or other heavy metals in the Pfizer mRNA vaccine. https://www.technologyreview.com/2020/12/09/1013538/what-are-the-ingredients-of-pfizers-covid-19-vaccine/
There is no genomic evidence at all that COVID-19 arrived before 2020 in the United States and therefore no hidden herd immunity:
Source:
There is no evidence SARS-CoV-2 was engineered, nor that it escaped a lab somewhere.
Source: https://www.washingtonpost.com/world/2020/01/29/experts-debunk-fringe-theory-linking-chinas-coronavirus-weapons-research/
Source: https://www.nature.com/articles/s41591-020-0820-9
Source: https://www.nationalgeographic.com/science/2020/05/anthony-fauci-no-scientific-evidence-the-coronavirus-was-made-in-a-chinese-lab-cvd/
There is no evidence a flu shot increases your COVID-19 risk.
Source: https://www.factcheck.org/2020/04/no-evidence-that-flu-shot-increases-risk-of-covid-19/
Source: https://academic.oup.com/cid/advance-article/doi/10.1093/cid/ciaa626/5842161
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A common request I'm asked is who I follow. Here's a public Twitter list of many of the sources I read.
https://twitter.com/i/lists/1260956929205112834
This list is biased by design. It is limited to authors who predominantly post in the English language. It is heavily biased towards individual researchers and away from institutions. It is biased towards those who publish or share research, data, papers, etc. I have made an attempt to follow researchers from different countries, and also to make the list reasonably gender-balanced, because multiple, diverse perspectives on research data are essential.
This is also available as an email newsletter at https://lunchtimepandemic.substack.com if you prefer the update in your inbox.
That NLP modeling article from Science is nifty. Only skimmed the abstract so far, but reminded me of some of John Holland's early Genetic Algorithms / Evolutionary Computing work.