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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From Dr. Angela Rasmussen on the origins of COVID-19. "While we can't rule out a laboratory origin for the COVID-19 pandemic, the evidence to date suggests zoonotic emergence. Objective investigations have been derailed by politics and conspiracy theories. I wrote this perspective piece in @NatureMedicine.
https://www.nature.com/articles/s41591-020-01205-5
Most serious scientists commenting on the matter have stated, as I have, that all possible origin hypotheses need to be investigated in an evidence-driven way. So far, there is no affirmative evidence of accidental or intentional lab origin.
Historically, epidemics are rarely due to a lab accident, either involving a natural or engineered pathogen. They are much more likely to occur through zoonotic spillover. There is genetic evidence that SARS-CoV-2 has natural origins. There is no evidence to support a lab leak.
Absence of evidence is not evidence of absence. This basic principle has been seized on by enthusiastic lab origin proponents. Overzealous activists, self-appointed detectives, unqualified writers, and politically motivated conspiracy theorists have converged under this banner.
And while we should objectively explore and investigate all possible hypotheses, the "I'm just asking questions, this is all very suspicious, what about (insert non-evidence here)" has been extremely harmful, both individually, to the scientific community, & to society as a whole
Arguing with the lab leak proponents is like talking to anti-vaxxers. They'll say they aren't conspiracy theorists, but then hit all the major conspiracy theory talking points:
-Answering questions with questions
-Strawman arguments about gain-of-function research & COI
-Presenting "evidence" that relies heavily on sinophobic stereotypes
-Ad hominem attacks (though I'll admit I laugh every time the term "knave" is used in this context)
-Using a "both sides" argument that implies scientists and conspiracy theorists are equally credible
-Digging around on the internet to cherry pick Twitter threads and out-of-context documentary evidence that people who collaborate are also friendly with each other, then present this as proof of a grand conspiracy. When this is pointed out, they say "I'm just asking questions!"
-Deeply misunderstanding fundamental virology. We've been cloning viruses and making chimeras and using reverse genetics systems for literally decades. The vast majority of this work is actually not "gain of function" or dual use research of concern.
-Deeply misunderstanding how gain-of-function research is actually regulated. Any GOF research funded by the US government is subject to heavy scrutiny and oversight, per federal law. You can't just take a NIH grant and start making more pathogenic/transmissible bat CoVs.
-Presenting media reports often containing unverifiable information as established fact
-Conflating complex geopolitical issues as further evidence ("China is secretive! Whistleblowers are silenced! It's EVIDENCE!")
-And so on and so on.
The reality is that there is no world pandemic police that can just serve China with a warrant & go search the freezers & archival records at the WIV which would potentially yield more insight as to the likelihood of lab origin. WHO & The Lancet are not law enforcement agencies.
And investigating zoonotic origins can take decades, and you may NEVER find the "smoking bat" or whatever other intermediate species that may be involved. It's like looking for a needle in a planet-sized haystack.
None of this means we shouldn't do an investigation or that we shouldn't consider all possible hypotheses, and by my estimation there are 3:
1. Zoonotic spillover
2. Lab accident
3. Intentional release
But we also shouldn't give these hypotheses equal weight, when the current evidence suggests one of these is more likely. We must investigate this objectively and let the evidence lead the way. Publicly proclaiming belief in the lab origin theories harms our ability to do this.
Robust debate is essential to sound science, but that debate should be informed by empirical evidence, not speculation based on pre-existing personal biases. Currently, this entire conversation has been derailed by the latter.
That will impair our ability to actually conduct the investigation that lab origin proponents are constantly clamoring for, and yet they seem unable to recognize that they are hindering, not helping, these efforts.
I urge everyone reading this to let the evidence lead the way, and to contribute to a climate that makes a fair & objective investigation possible. Call conspiracy theories what they are, distinguish between politics and science, and push back against this harmful misinformation.
A pandemic is by definition a global crisis. Telling the true story of its origin will require global cooperation. We can't move forward collaboratively without trust, and that is eroded by when personal bias and conspiracy theories are given equal weight as objective inquiry."
Source:
Source: https://www.nature.com/articles/s41591-020-01205-5
Commentary: A tremendous amount of the speculation about the origin of COVID-19 is politically motivated. Keep politics out of it and stay focused solely on the science - and acknowledge we may not know for years, if ever, where it came from. No one can say where influenza or measles came from, for example. They've always just been a part of life on earth for humans.
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NSAIDs may be a double-edged sword. "Public health officials have raised concerns about the use of nonsteroidal anti-inflammatory drugs (NSAIDs) for treating symptoms of coronavirus disease 2019 (COVID-19). NSAIDs inhibit the enzymes cyclooxygenase-1 (COX-1) and cyclooxygenase-2 (COX-2), which are critical for the generation of prostaglandins – lipid molecules with diverse roles in homeostasis and inflammation. Inhibition of prostaglandin production by NSAIDs could therefore have multiple effects on COVID-19 pathogenesis. Here, we demonstrate that NSAID treatment reduced both the antibody and pro-inflammatory cytokine response to SARS-CoV-2 infection. The ability of NSAIDs to modulate the immune response to SARS-CoV-2 infection has important implications for COVID-19 pathogenesis in patients. Whether this occurs in humans and whether it is beneficial or detrimental to the host remains an important area of future investigation. This also raises the possibility that NSAIDs may alter the immune response to SARS-CoV-2 vaccination."
Source: https://jvi.asm.org/content/early/2021/01/12/JVI.00014-21
Commentary: This bears very serious investigation. NSAIDs could be used to mitigate the cytokine storm immune response, but it also means that if NSAIDs - like ibuprofen and acetaminophen - suppress immune responses, we should be studying just how much. Given the consumption of painkillers in the general population, a whole bunch of people could be making their vaccinations less effective.
There's no definitive answer yet, but in general it's good advice that if you don't NEED to take medication - especially over the counter, self-administered like ibuprofen - don't. Obviously, if your healthcare provider has prescribed medication for you, follow their guidance, but if you've got a headache at the end of the day, consider non-pharmaceutical interventions first.
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More on the new strains from Dr. Emma Hodcroft:
"There's been a lot of news today about 'new variants in Brazil' & 'S:E484' and 'Ohio variants'. A short thread discussing what we know about each.
There are two variants circulating in Brazil: 20J/501Y.V3, recently detected in Japan & prevalent in Manaus. And temporarily-labelled '20B/S.484K', a larger clade circulating more widely in Brazil.
They both carry the spike mutation 484K, though this arise separately.
S:E484K is also found in 501Y.V2 (primarily circulating in South Africa).
Why are we particularly concerned about S:E484K? You can read more at CoVariants.org, as discussed in a tweet from earlier this week:
The focal build for S:E484 is updated with data from 13 Jan & includes the sequences from Manaus, Brazil which cluster with the recent Japanese travel sequences in new Nextstrain clade 20J/501Y.V3:
20J/501Y.V3 sequences have both 484K & 501Y (like 501Y.V2, mostly in South Africa) - they are shown in orange below.
They are clearly separate from the other, larger S:E484K cluster circulating in Brazil (in green, with temporary label 20B/S.484K)
In divergence (mutation) view, the 501Y.V3 variant has a 'long branch' - it sticks out to the right. This means it has a high number of mutations relative to surrounding sequences.
Zooming in, we can see that the Japanese samples are nested within the Brazilian diversity.
There have also been some news reports circulating about 2 'Ohio variants'.
From press release data, one is a 20G clade sequence with S:N501Y. As shown below (blue) 501Y mutations have popped up in the past. While worth keeping an eye on, I think this isn't so remarkable.
The other variant identified seems to have 3 mutations, 1 each in the Spike, Membrane, & Nucleocapsid proteins in a 20G background. There are 17 USA seqs with the same mutations (Only 1 of these is currently visible in N America Nextstrain build).
The Ohio samples are not yet online, but the 17 existing samples that seem to have the same mutations are from Massachusetts, Maryland, Minnesota, New York, Texas, & Wisconsin.
Another USA-state focused build captures 5 of them, all dating between 9 Dec & 12 Jan.
The preprint states that in Columbus, OH, at end of Dec, the variant went from 10% prevalence to 60% prevalence (10-20 samples per week) in 3 weeks.
I'd be curious to hear if other states have seen this variant & if so, also if they've seen similar rises.
I have been careful here not to mention the mutations as, so far as I can tell, the preprint is not yet out. I'll update with a link to the preprint & the exact mutations when I hear it's up."
Source:
Commentary: It is concerning but unsurprising that a new strain with similar mutations along the N501Y sequence may have independently emerged in the United States. The country has done an incredibly poor job of controlling the pandemic, and with more cases come more mutations. We are seeing mutations centering around sequences E484K and SN:501Y (including B.1.1.7), and these strains appear to have increased transmissibility.
With a new American strain combined with the E484K first detected in Brazil, and the SN:501Y B.1.1.7 strain first detected in the UK and the SN:501Y.V2 first detected in South Africa, we now have multiple strains of SARS-CoV-2 floating around with increased transmissibility. The virus is adapting fast. We are not keeping up.
So what do we need to do? Wherever we live, press legislators and elected officials to move mountains and make vaccination a top national priority everywhere. Get vaccines into people as quickly as possible. We have to put out the fire fast, before it grows beyond our ability to slow it down.
As for daily life, be wearing the best mask available to you outside your home, always.
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Prepare for a fourth wave in the United States. "According to Bedford, the U.S. still has about two months to prepare for — and slow down — the variant. On the surface, that timeline sounds like good news. But, the findings are worrying, Bedford says. They mean the steep rise in cases and hospitalizations that is already happening in some states can't be blamed on a more contagious virus.
"I think it's not at all really conceivable that this more transmissible variant has contributed to surging cases in the U.S. this fall and winter, " he says. "We're kind of just barely getting started with this variant."
Yet the outbreak in the U.S. is the worst it's ever been. The U.S. reported its most deadly day of the pandemic on Tuesday, with a record 4,327 people dying of COVID-19. Each week, more than 1.5 million people test positive for the virus across the country. Several states, like California, Arizona and Rhode Island have some of the highest infection rates in the world.
The U.S. needs to be thinking about how to minimize damage from this new variant, right now, Hodcroft says. "This is our early warning. Because by the time you have something spreading exponentially in your country, it is much harder to get it under control."
What needs to be done will be different for each community. Activities that seemed relatively safe before — like outdoor dining --- might not be as safe with the new version of the virus.
Communities should start thinking about acquiring better masks or suggesting to people ways they can improve their masks.
Cities and states can ramp up testing and contact tracing. They can start contact tracing the variant to try and slow down its spread. And finally, the entire country needs to focus on vaccinating people as quickly as possible.
Otherwise Bedford says, in March we will likely see another wave of the virus.
"I was expecting that by around March, things would be getting decently under control in the United States," he says, because the weather would warm up and more people would be immune, through the vaccine or natural exposure.
"Those factors will bring the previous version of the virus under control," he says, but not the new variant. "My expectation now is that we end up with a spring wave of this new variant virus.""
Source: https://www.npr.org/sections/health-shots/2021/01/13/956504515/u-k-variant-could-drive-a-new-surge-in-the-u-s-experts-warn
Commentary: The new strains have spread in strict lockdowns in the UK and Ireland. How well will they spread in a country like the United States, where precautions are already lax?
Be prepared for a fourth surge.
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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.