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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Background on the UK variant. "On 8 December, during a regular Tuesday meeting about the spread of the pandemic coronavirus in the United Kingdom, scientists and public health experts saw a diagram that made them sit up straight. Kent, in southeastern England, was experiencing a surge in cases, and a phylogenetic tree showing viral sequences from the county looked very strange, says Nick Loman, a microbial genomicist at the University of Birmingham. Not only were half the cases caused by one specific variant of SARS-CoV-2, but that variant was sitting on a branch of the tree that literally stuck out from the rest of the data. “I’ve not seen a part of the tree that looks like this before,” Loman says.
Less than 2 weeks later, that variant is causing mayhem in the United Kingdom and elsewhere in Europe. Yesterday, U.K. Prime Minister Boris Johnson announced stricter lockdown measures, saying the strain, which goes by the name B.1.1.7, appears to be better at spreading between people. The news led many Londoners to leave the city today, before the new rules take effect, causing overcrowded railway stations. The Netherlands, Belgium, and Italy announced they were temporarily halting passenger flights from the United Kingdom. The Eurostar train between Brussels and London will stop running tonight at midnight, for at least 24 hours.
But scientists have never seen the virus acquire more than a dozen mutations seemingly at once. They think it happened during a long infection of a single patient that allowed SARS-CoV-2 to go through an extended period of fast evolution, with multiple variants competing for advantage.
One reason to be concerned, Rambaut says, is that among the 17 mutations are eight in the gene that encodes the spike protein on the viral surface, two of which are particularly worrisome. One, called N501Y, has previously been shown to increase how tightly the protein binds to the angiotensin-converting enzyme 2 receptor, its entry point into human cells. The other, named 69-70del, leads to the loss of two amino acids in the spike protein and has been found in viruses that eluded the immune response in some immunocompromised patients.
But scientists say B.1.1.7 may already be much more widespread. Researchers in the Netherlands have found it in a sample from one patient taken in early December, Dutch health minister Hugo de Jonge wrote in a letter to Parliament today. They will try to find out how the patient became infected and whether there are related cases. Other countries may have the variant as well, says epidemiologist William Hanage of the Harvard T.H. Chan School of Public Health; the United Kingdom may have just picked it up first because it has the most sophisticated SARS-CoV-2 genomic monitoring in the world. Many countries have little or no sequencing."
Source: https://www.sciencemag.org/news/2020/12/mutant-coronavirus-united-kingdom-sets-alarms-its-importance-remains-unclear
Source: https://virological.org/t/preliminary-genomic-characterisation-of-an-emergent-sars-cov-2-lineage-in-the-uk-defined-by-a-novel-set-of-spike-mutations/563
Commentary: Scientists are speculating - and it's speculation at this point - that the mutations may be occurring in chronic sufferers; in the pre-print paper listed above, they also speculate that convalescent plasma may have played a role.
Regardless, there doesn't appear to be any new functionality that would negate our current protective measures. Wearing a mask appears to be just as effective against the N501Y variant as it is against the current D614G variant. What the new variant may - emphasis on may - do is make it easier to catch COVID-19 if you're not wearing a mask or not wearing it properly, as the speculated receptor change may make it easier to latch on once it's inside your nose and mouth.
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Dr. Scott Gottlieb on the new variant. "Well, it's probably not more lethal, but we don't fully understand its contours. There was a question of whether or not this there is a new variant as a question of whether or not it's become the predominant strain in London because of what we call founders effect. It just got into London and got into some early super spreading events. Whether or not it's the result of what we call selective pressure it's being selected for because it has qualities that make it more likely to spread. Increasingly it does seem to be the latter, it seems like this new strain is more contagious. It doesn't seem to be any more virulent any more dangerous than run of the mill COVID. The next question is will it obviate our natural immunity? So will people who had COVID from the old strain be able to get this new strain or will it obviate vaccines? And the answer is probably not. This virus mutates, like all viruses flu vaccine mutates flute mutates the most and what viruses do is they change their surface proteins. And once they do that the antibodies that we've developed against those surface proteins no longer work. Now flu mutates very rapidly changes at surface proteins very rapidly. So we constantly need to get a new flu shot. Some viruses like measles don't change their surface proteins. And so the measles shot we got 20 years ago still works Coronavirus, seems somewhere in the middle. It's going to mutate and changes surface proteins but probably slow enough that we can develop new vaccines."
Source:
Commentary: One of the saving graces of the new mRNA vaccines is that as mutations occur, it should be relatively straightforward to continue adapting our vaccines to accommodate the mutations, particularly on the spike protein. In a greatly oversimplifed explanation, the mRNA vaccine is kind of like a jigsaw puzzle. Imagine a contagious SARS-CoV-2 virus as the completed, whole puzzle. The vaccine is basically some key features of the puzzle, broken up, and stirred. Imagine the corners and edge pieces of the jigsaw puzzle, if you will - that's more or less what's in the mRNA vaccine. It helps our bodies recognize the real thing faster and clean it out faster.
Now, if a mutation occurs, scientists need to change out the affected corner and edge pieces for the changed ones, but unlike traditional vaccines, these swapouts should be much, much faster. A mutation that is substantial could only take a few weeks to adapt an mRNA vaccine, whereas a traditional vaccine could take months to adapt.
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Surgeon General Jerome Adams on racial disparities. "Well, I'm the United States Surgeon General, but make no mistake about it. I'm a African American, I grew up poor, black rural, I know that long before COVID there were many diseases, hypertension, cancer, diabetes that were plaguing communities of color, and COVID just unveiled those disparities that have been around for a long time. I've talked previously about the the history of mistreatment of communities of color, the Tuskegee experiments, the terrible treatment of Henrietta Lacks his and her family and how they just took herself without her permission. We need to understand that that this trust comes from a real place. It actually comes from my office, several surgeons general oversaw for 40 years, the Tuskegee studies where treatment was denied to black men, and I walk past their pictures every single day, when I go into my office. So believe you me, this legacy is important to me, and helping restore that trust is important. We've had many people involved in the review, and actually a study participants of color. And what what I want to tell people most of all, is I walked the talk, I got vaccinated on Friday. I actually feel great. You know, my mother in law and my mother are watching and they've been asking me all we can How are you feeling? I feel great. And I hope people will get the vaccine based on information that they get from training. trusted resources because it's okay to have questions. What's not okay is to make poor health decisions based on misinformation."
On immigration status:
"I want to reassure people that your information when collected to get your second shot, if you get the Pfizer or Moderna vaccine will not be used in any way, shape, or form to harm you legally. That is something that I've been assured of. And we tell people that all the time when they need to come in for emergency care or public health care. So we're going to work with states and local officials and trusted organizations to make sure everyone gets the information they need and feel safe coming in to get vaccinated because that's how we end this pandemic. That's the good news. There is a light at the end of this dark tunnel and we just need to keep running to it."
Source:
Commentary: The latter is critical. The virus doesn't care what your legal status is. If you're a living human, it will try to infect you. If we have reserves of people who refuse the vaccine, we create reservoirs for the virus to lurk in, and that increases the risk to everyone. The longer the virus stays substantially in circulation, the more at-bats it gets to mutate. Shut it down by vaccinating as many people as quickly as possible.
Think of it this way. Suppose you had a reasonably small fire in front of you and a bucket of water. What would be more effective, throwing random teaspoons of water at the fire, or pouring the whole bucket on it at once? The latter tends to work better.
If we piecemeal and half-ass the vaccine distribution, the virus gets to fight back more easily by adapting and mutating. If we deal it a solid one-two punch by wearing masks and vaccinating like crazy, we'll have it on the ropes sooner rather than later.
A reminder of the simple daily habits we should all be taking.
1. Wash/sanitize your hands every time you are in or out of your home for any reason. Consider also spraying the bottoms of your shoes with a general disinfectant (alcohol/bleach/peroxide) when you return home. Remember that cleaners are NEVER to be ingested or injected. If you come in physical contact with others, wash your clothing upon returning home.
2. Always wear a mask when out of your home and if going to a high-risk area, wear goggles. Respirators are back in stock at online retailers, too. When going indoors to a place that isn't your home, wear the best protective mask available to you.
3. 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.
4. Get your personal finances in order now. Cut all unnecessary costs.
5. Replenish your supplies as you use them. Avoid reducing your stores to pre-pandemic levels in case an outbreak causes unexpected supply chain disruptions.
6. 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).
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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.