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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Commentary: Anyone who's ever built a bonfire or campfire knows that putting it out is never simple, not if you want to do it safely. You can't just throw a bucket of water on it and call it a night. That's not how fires work. You have to dig into it, water it thoroughly, break up large chunks of embers, etc. until you're sure the fire is out and you can safely sift your hands through the ashes without getting burned. That's how you know it's out.
The recent decline in cases of COVID-19 is a welcome change, but it doesn't mean the fire's out. We're making good progress on the existing COVID-19 infections - putting out the obvious fire and flames. But if we stop our countermeasures - which too many places are doing - we're walking away from a bed of coals that are still hot and growing hotter. The new strains - B.1.1.7, B.1.351, P.1 - are growing under the radar. As they achieve critical mass, they'll create a fourth surge - and places which do not maintain countermeasures will be at even greater risk.
What does putting the COVID-19 fire out completely mean? It means a few more months of rapid, intense vaccination as fast as possible. It means a few more months of school at home, of takeout instead of dining in, a few more months of wearing a mask everywhere. If we do this, regardless of what our governments say, we will be helping put out the fire properly. If we become lax in our precautions, the embers will flare to new life again.
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The P.1 strain is showing signs of strength. "Cases of SARS-CoV-2 infection in Manaus, Brazil, resurged in late 2020, despite high levels of previous infection there. Through genome sequencing of viruses sampled in Manaus between November 2020 and January 2021, we identified the emergence and circulation of a novel SARS-CoV-2 variant of concern, lineage P.1, that acquired 17 mutations, including a trio in the spike protein (K417T, E484K and N501Y) associated with increased binding to the human ACE2 receptor. Molecular clock analysis shows that P.1 emergence occurred around early November 2020 and was preceded by a period of faster molecular evolution. Using a two-category dynamical model that integrates genomic and mortality data, we estimate that P.1 may be 1.4–2.2 times more transmissible and able to evade 25-61% of protective immunity elicited by previous infection with non-P.1 lineages. Enhanced global genomic surveillance of variants of concern, which may exhibit increased transmissibility and/or immune evasion, is critical to accelerate pandemic responsiveness."
Source: https://github.com/CADDE-CENTRE/Novel-SARS-CoV-2-P1-Lineage-in-Brazil/blob/main/manuscript/FINAL_P1_MANUSCRIPT_25-02-2021_combined.pdf
Commentary: For reference, the B.1.1.7 strain shows an increased infectivity rate between 43-90%. P.1's rate of 140-220% is dramatically larger, and a serious problem as it gains new footholds.
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B.1.1.7 confirmed 43-90% more transmissible. "A novel SARS-CoV-2 variant, VOC 202012/01 (lineage B.1.1.7), emerged in southeast England in November 2020 and is rapidly spreading toward fixation. Using a variety of statistical and dynamic modelling approaches, we estimate that this variant has a 43–90% (range of 95% credible intervals 38–130%) higher reproduction number than preexisting variants. A fitted two-strain dynamic transmission model shows that VOC 202012/01 will lead to large resurgences of COVID-19 cases. Without stringent control measures, including limited closure of educational institutions and a greatly accelerated vaccine roll-out, COVID-19 hospitalisations and deaths across England in 2021 will exceed those in 2020. Concerningly, VOC 202012/01 has spread globally and exhibits a similar transmission increase (59–74%) in Denmark, Switzerland, and the United States."
Source: https://science.sciencemag.org/content/early/2021/03/02/science.abg3055
Commentary: This news was first reported in December but just passed peer review, locking in these transmission numbers.
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Who has been most impacted? A new pre-print paper from UCSF: "Using death records from the California Department of Public Health, we estimated excess mortality among Californians 18–65 years of age by occupational sector and occupation, with additional stratification of the sector analysis by race/ethnicity. During the COVID-19 pandemic, working age adults experienced a 22% increase in mortality compared to historical periods. Relative excess mortality was highest in food/agriculture workers (39% increase), transportation/logistics workers (28% increase), facilities (27%) and manufacturing workers (23% increase). Latino Californians experienced a 36% increase in mortality, with a 59% increase among Latino food/agriculture workers. Black Californians experienced a 28% increase in mortality, with a 36% increase for Black retail workers. Asian Californians experienced an 18% increase, with a 40% increase among Asian healthcare workers. Excess mortality among White working-age Californians increased by 6%, with a 16% increase among White food/agriculture workers."
Source: https://www.medrxiv.org/content/10.1101/2021.01.21.21250266v1.full.pdf
Commentary: While disappointing, it's unsurprising to see minorities with substantially higher excess mortality as well as food and service workers. If reducing deaths and ICU cases is the priority, then vaccination needs to follow the numbers - food and agriculture workers should be vaccinated quickly and early, and Latino and Black populations prioritized.
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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. Wear an N95/FFP2/KN95 that's NIOSH-approved or better mask if you can obtain it. If you can't get an N95 mask, wear a surgical mask with a cloth mask over it.
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. Masks must fit properly to work. Here's 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.