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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Another case of reinfection. "42-year-old healthy male military healthcare provider presented with cough, subjective fever, and myalgias on 21 March following a workplace COVID-19 exposure and tested positive by SARS-CoV-2 RT-PCR (Figure 1). Physical examination was unrevealing and supportive outpatient management was pursued [4]. Clinical resolution of illness occurred by day 10, and he returned to baseline excellent health for the following 51 days
A partial genome sequence was obtained from the initial clinical infection, consisting of sequence fragments totaling 4,126 bp and distributed across the genome. Sequencing of the sample from the patient’s second illness yielded a nearly coding complete genome of 27,268 bp. One discrete 50 bp region of zero coverage was observed. Phylogenetic analysis placed this virus in lineage B.1.26 and the genome encoded the D614G variation in the spike protein [8]. Comparison of the partial sequence obtained from the initial infection with the nearly complete sequence obtained from the re-infection identified several potential variations, including one high confidence variation.
The clinical, epidemiological, and sequencing data of this case suggest early re-infection with SARSCoV-2, only 51 days after resolution of initial infection. Importantly, this was observed in a young immunocompetent patient. In contrast to the case reported by To et al., this second infection was more severe, potentially due to immune enhancement, acquisition of a more pathogenic strain, or perhaps a greater inoculum of infection as the second exposure was from within the household."
Source: https://academic.oup.com/cid/advance-article/doi/10.1093/cid/ciaa1436/5908892
Commentary: The genomic drift is how we know it was reinfection and not just an infection that never went away. The reason why the reinfection was more severe hasn't been determined yet, but the time period was 51 days between infections, which coincides with reports from yesterday about detectable antibodies in serological assays fading after two months.
Thus, if you or someone you know has had COVID-19, you have no guarantee you won't contract it again. Protect yourself as though you never had it to begin with.
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Face shields alone are ineffective. "Plastic face shields are almost totally ineffective at trapping respiratory aerosols, according to modelling in Japan, casting doubt on their effectiveness in preventing the spread of coronavirus.
A simulation using Fugaku, the world’s fastest supercomputer, found that almost 100% of airborne droplets of less than 5 micrometres in size escaped through plastic visors of the kind often used by people working in service industries.
One micrometre is one millionth of a metre.
In addition, about half of larger droplets measuring 50 micrometres found their way into the air, according to Riken, a government-backed research institute in the western city of Kobe."
Source: https://www.theguardian.com/world/2020/sep/22/face-shields-ineffective-trapping-aerosols-japanese-supercomputer-coronavirus
Commentary: No surprises here. Masks on, please.
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Bone marrow impact. "Even bone marrow may not be a safe harbor from the ravages of COVID-19, according to a study that found previously unrecognized changes in newly produced immune cells, called monocytes, released into the blood from bone marrow. To learn more about how the body responds to COVID-19, researchers obtained serial "snapshots" of patients' immune health by analyzing their immune cells at multiple points during their hospital stays. In COVID-19 patients with more severe disease, the monocytes do not function properly, researchers reported last week in Science Immunology. It was not yet clear whether the monocytes are being released from the bone marrow in an altered state or whether the alterations happen after monocytes enter the blood, coauthor Tracy Hussell of the University of Manchester in the UK told Reuters. Either way, she said, treatments that prevent their release from the bone marrow may help reduce the exaggerated immune response that contributes to poor outcomes in patients with severe COVID-19."
"Here, by analyzing fresh blood samples immediately without prior storage we outline unappreciated immune abnormalities present within COVID-19 patients. Assessment of inflammatory mediators within the blood demonstrated these immune properties were most dysregulated in patients with severe COVID-19 prior to admission to intensive care, indicating immune modulating therapies should be considered early after admission. Furthermore, our study demonstrated profound alterations in the myeloid cells of COVID-19 patients. Our data demonstrate that monocytes from COVID-19 patients displayed elevated levels of the cell cycle marker Ki-67 but reduced expression of the prostaglandin-generating enzyme COX-2, with both these features being predominant in severe COVID-19 patients. These findings not only identify possible immune biomarkers for patient stratification but potential mechanisms of immune dysfunction contributing to the immunopathology of COVID-19."
Source: https://www.reuters.com/article/us-health-coronavirus-science-idUSKCN26C2X1
Source: https://immunology.sciencemag.org/content/5/51/eabd6197
Commentary: Yet another bodily system impacted by the SARS-CoV-2 virus. We will be decoding the health impacts of a COVID-19 infection for years, maybe even decades, to come.
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Assisted living facility fatality rates as high as 31.6%. "State case fatality ranged from 3.32% in North Carolina to 9.26% in Connecticut, but for ALs in these states it was 12.89% and 31.59%, respectively. Among ALs with at least 1 case, mid‐size communities had fewer cases (IRR=0.829; p=0.004), than very small ALs. ALs with higher proportions of racial/ethnic minorities had more COVID‐19 cases (IRR=1.08; p<0.001), as did communities with higher proportions of residents with dementia, COPD and obesity."
Source: https://onlinelibrary.wiley.com/doi/abs/10.1111/jgs.16850
Commentary: COVID-19 was deadly at a rate of 1 in 3 people in Connecticut's assisted living facilities. When someone asks why they should be concerned, it's because it is incredibly dangerous to those who are at high risk. If you have a relative in such a facility, inspect it carefully and frequently to ensure they are mitigating risks appropriately, especially with ventilation.
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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.
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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.