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.
You are welcome to share this.
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Dr. Fauci on targeting the virus in an AMA interview.
"AMA: You know, this is maybe a bit of a theoretical question. But it's noted that, you know, knowing the, the what we do about the biology of the virus, you know, the spike protein seems to be something that one would go after. And if one were devising a vaccine toward a surface element, it would be hands down logical to go in that direction. So you know, every company you can imagine, thinking that way, but when you think of the worldwide portfolio of vaccines, is it wise or not to have the vaccine dominated by one target?
AF: The answer is no. But this target is so clearly important in the binding of the virus to its cellular receptor, which is the h2 receptor, that you would have to have the predominant effort being using the spike protein receptor binding domain as the target of the neutralizing antibody. But you're absolutely right. You never want to put all your eggs in one basket. And that's the reason why the next generation of vaccines certainly will include something above and beyond the receptor binding domain of the spike protein, but you would really have to go with that first. And predominantly from everything we know, in animal studies, and even in the in in vitro physiology."
Source:
Commentary: One of the reasons we haven't seen much mutation in SARS-CoV-2 so far beyond the D614G mutation is that there's been no survival advantage to any mutations. We as a species still have no native immunity to it, nor do we have any pharmaceutical interventions to stop it right now. As vaccines deploy over the next year, that may change.
The concern here in the AMA interview is that by targeting just the large protein spike on SARS-CoV-2, a mutation to that spike could render vaccines ineffective - a higher risk once the vaccines are in the field. That's why the next wave of vaccines will hopefully be able to accommodate it.
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Shocking longer-term outcomes. "Although characteristics and in-hospital outcomes for persons with coronavirus disease 2019 (COVID-19) have been well described, less is known about the longer-term outcomes of hospitalized patients.
Of 1648 patients with COVID-19 admitted to 38 hospitals, 398 (24.2%) died during hospitalization and 1250 (75.8%) survived. Of 1250 patients discharged alive, 975 (78.0%) went home whereas 158 (12.6%) were discharged to a skilled nursing or rehabilitation facility (Table 1).
By 60 days after discharge, an additional 84 patients (6.7% of hospital survivors and 10.4% of intensive care unit [ICU]-treated hospital survivors) had died, bringing the overall mortality rate for the cohort to 29.2%, and 63.5% for the 405 patients who received treatment in an ICU.
Within 60 days of discharge, 189 patients (15.1% of hospital survivors) were rehospitalized.
Cardiopulmonary symptoms (such as cough and dyspnea) were reported by 159 patients, including 92 with new or worsening symptoms and 65 with persistent loss of taste or smell. Fifty-eight patients reported new or worsening difficulty completing activities of daily living. Among 195 patients who were employed before hospitalization, 117 had returned to work whereas 78 could not because of ongoing health issues or job loss. Of the 117 patients who returned to work, 30 reported reduced hours or modified duties due to health reasons.
Nearly half of all patients (238 of 488) reported being emotionally affected by their health, and 28 sought care for mental health after discharge. Moreover, 179 patients reported at least a mild financial impact from their hospitalization, with 47 reporting use of most or all of their savings and 35 rationing food, heat, housing, or medications due to cost."
Source: https://www.acpjournals.org/doi/10.7326/M20-5661
Commentary: We are objectively getting better at preventing COVID-19 deaths. But what happens in the long run? Depleted savings, financial strain, mental health issues, long term disability - and these are the survivors, the people who "recovered" from COVID-19.
This is one of the reasons why prevention is so vital. Yes, you probably will survive COVID-19, based on the odds. But nothing says your recovery will be timely, complete, or without substantial challenges.
Consider that potential outcome versus the simplicity of staying home and wearing a mask whenever you're not at home.
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One potential reason why women fare better? Neutrophils. "Women and men have striking differences in their autoimmune disease risk, their predisposition to and prognosis with various cancers, and their ability to respond to some infections—including the novel coronavirus. New research offers a potential explanation for these distinctions: sex-based differences in neutrophils, humans’ most common circulating immune cells.
“In general, women have a more robust immune response to vaccines and certain infections as well as decreased risk for certain cancers, potentially driven by better immune surveillance,” Mariana J. Kaplan, MD, chief of the systemic autoimmunity branch of the National Institute of Arthritis and Musculoskeletal and Skin Diseases (NIAMS), explained in an interview.
Most recently, clinicians have noted better outcomes for women than men with coronavirus disease 2019 (COVID-19), including lower rates of hospitalizations, intensive care unit admissions, and fatalities. “Conversely, enhanced immune responses in females may promote higher susceptibility to inflammatory and autoimmune diseases like systemic lupus erythematosus, Sjögren syndrome, and rheumatoid arthritis,” Kaplan said.
Neutrophils, white blood cells that defend against invading microorganisms, could play a role in this. Kaplan and her colleagues previously showed that healthy young men’s neutrophils were more immature and less activated than those of similar women. To carry these findings further and uncover potential mechanisms involved, the team’s latest study assessed male and female neutrophil gene expression patterns and functional characteristics.
The researchers performed RNA sequencing on circulating neutrophils and other immune cells from 39 healthy adult women and men. They found that women’s neutrophils displayed higher expression of type I interferon (IFN)–stimulated genes, suggesting an enhanced response to this group of crucial antiviral cytokines.
“We were surprised to detect upregulation of a particular arm of the immune pathway—the increased response to type I IFNs that is so critical in infection responses and in the pathogenesis of many autoimmune diseases,” lead author Sarthak Gupta, MD, an assistant research physician at NIAMS, said in an interview. No other immune cell types displayed similar sex-associated differences in IFN responses, he said, which made the finding particularly intriguing."
Source: https://jamanetwork.com/journals/jama/fullarticle/2771227
Commentary: It may be possible down the road to genetically edit neutrophils to create a more robust immune response overall, and in men in particular.
One of the outcomes I am hopeful for from COVID-19 is that it creates large leaps in progress for medicine, the same way wars have substantially advanced technology gains afterwards. What we've learned in the last 9 months could propel research and medical gains for years to come, once we're out of this and we have a moment to breathe.
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Culling of minks: reasonable? "Animal experiments have shown that non-human primates, cats, ferrets, hamsters, rabbits and bats can be infected by SARS-CoV-2. In addition, SARS-CoV-2 RNA has been detected in felids, mink and dogs in the field. Here, we describe an in-depth investigation using whole genome sequencing of outbreaks on 16 mink farms and the humans living or working on these farms. We conclude that the virus was initially introduced from humans and has since evolved, most likely reflecting widespread circulation among mink in the beginning of the infection period several weeks prior to detection. Despite enhanced biosecurity, early warning surveillance and immediate culling of infected farms, transmission occurred between mink farms in three big transmission clusters with unknown modes of transmission. Sixty-eight percent (68%) of the tested mink farm residents, employees and/or contacts had evidence of SARS-CoV-2 infection. Where whole genomes were available, these persons were infected with strains with an animal sequence signature, providing evidence of animal to human transmission of SARS-CoV-2 within mink farms."
Source: https://science.sciencemag.org/content/early/2020/11/09/science.abe5901
Commentary: The culling of minks is a reasonable choice given these results. When a virus crosses species, it increases chances for mutation. When a virus enters a new population and runs rampant, mutation increases.
Mutation is like playing telephone - every subsequent transmission changes the virus a tiny little bit. Most of the time, the mutations are harmless. Sometimes, they're not. But when a mink farm has millions of mink, and they all get infected, it's like infecting an entire nation all at once and the chances of new mutations are dramatically higher just because there are so many more individuals who could be infected.
Culling them, as awful as it sounds, may be the right choice to prevent a disease reservoir as well as rapid mutation of the virus.
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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.
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.
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. Participate in your local political process. For Americans, go to Vote.org and register/verify your vote.
7. Ventilate your home as frequently as weather and circumstances permit.
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Common misinformation debunked!
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.