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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On schools reopening. "Abstract: Reopening schools is an urgent priority as the COVID-19 pandemic drags on throughout much of the world. To explore the risks associated with returning to in-person learning and the value of mitigation measures in a school setting, we use the stochastic, network-based SEIRS+ epidemiological modeling platform to simulate SARS-CoV-2 transmission in schools. Because children and adolescents differ both in disease susceptibility and in patterns of social interaction, we use distinct models of SARS-CoV-2 transmission for primary and secondary school settings. We find that a number of mitigation measures may prove useful, particularly when community prevalence is low. Student cohorting, in which students are divided into two separate populations that attend in-person classes on alternating schedules, can reduce both the likelihood and the size of outbreaks. Proactive testing of teachers and staff once or twice a week can help catch introductions early, before they spread widely through the school. Especially in secondary schools, once- or twice- weekly testing amongst students should also be considered to further reduce the likelihood of a large outbreak amongst the full population. Vaccinating teachers and staff protects these individuals and may also have a disproportionate protective effect on the outbreak potential in primary and secondary schools when vaccines block SARS-CoV-2 transmission in addition to symptoms. Other mitigation strategies – including mask-wearing, social distancing, and increased ventilation – remain a crucial component of any reopening plan."
Source: https://www.color.com/wp-content/uploads/2021/01/K12model.pdf
Commentary: Secondary schools - high schools - are much bigger vectors for spread because of the way classes are organized. Students mix with each other much more. Primary schools tend to have fewer large outbreaks because they naturally form classroom-size cohorts with less mixing of students. To reopen schools safely, vaccines, NPIs, and cohorting may be the necessary way to go.
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When will we be able to safely reopen? "The finding “passes the gut check,” said Trevor Bedford, a geneticist at the Fred Hutchinson Cancer Research Center and the University of Washington. He said the pace of vaccine rollout was an unknown that could change the conclusions. The Biden administration has said it intends to accelerate distribution, but those assertions have yet to be tested.
Dr. Bedford also cautioned that a new variant of the virus that recently emerged from the United Kingdom and that is believed to be more transmissible than others circulating in the United States “could cause more of a spring wave than what was modeled here.”
Lauren Ancel Meyers, a professor of biology and statistics at the University of Texas at Austin, said that Dr. Shaman’s reasoning “all makes intuitive sense.” Dr. Meyers said she agreed that the uncontrolled outbreaks in many places in 2020 have lowered the benefits of a vaccine.
“Unfortunately, we've let this virus spread extensively and are launching the vaccination campaign at the height of the threat,” Dr. Meyers said. “The more the virus spreads before the vaccine reaches people, the fewer deaths we can prevent with the vaccine.”
Dr. Meyers added, though, that mortality figures could come down sooner than infections with the right vaccination strategy, perhaps allowing some parts of the country to open up more quickly than expected. That depends on highly exposed frontline workers and those who are most at risk of death getting vaccinated quickly, she said.
“We may get to the point where, even though the virus is still spreading, it’s just less deadly on a population level and policymakers feel comfortable relaxing some of the measures we now have in place to protect our health care systems and save lives,” Dr. Meyers said.
Over all, the findings are probably unwelcome news for millions of people who would like to return to normal life, from a guilt-free night out at a restaurant to chatting about football scores at school dropoff, as soon as possible.
Policymakers who will have to lay down and sometimes enforce those restrictions in 2021 are already aware of the long haul still ahead, said Mayor Jenny A. Durkan of Seattle in an interview.
“I think that the modeling is absolutely credible,” said Ms. Durkan, who has received praise for incorporating science into her own policy decisions. The mayor said she was preparing Seattle to continue social distancing measures “at least through the summer and probably into the fall.”"
Source: https://www.nytimes.com/interactive/2021/01/24/us/covid-vaccine-rollout.html
Commentary: Most of the current models show the pandemic coming to an end at a large scale by the end of the summer. The new strains could accelerate that time-table, at the tradeoff of many more deaths. The wild card will be strains like E484K and not-yet-discovered strains that can adapt to the vaccine and previous infections. Either way, you'll be wearing a mask outside your home for quite some time to come. Plan on wearing a mask, regardless of circumstances, until 2022 at the very least. Do look forward to the holiday season this year - by the time it rolls around, most people who want a vaccine will have gotten one, and you can safely gather with loved ones in the privacy of someone's home.
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How long can someone remain contagious? "Background Immunocompromised patients show prolonged shedding of SARS-CoV-2 in nasopharyngeal swabs. We report a case of a prolonged persistence of viable SARS-CoV-2 associated with clinical relapses of COVID-19 in a lymphoma patient. Methods Nasopharyngeal swabs and blood samples were tested for SARS-CoV-2 by Real time-PCR (RT-PCR). On five positive nasopharyngeal swabs, we performed viral culture and next generation sequencing. We analysed the patient's adaptive and innate immunity to characterize T and NK cell subsets. Findings SARS-CoV-2 RT-PCR on nasopharyngeal swabs samples remained positive with cycle threshold mean values of 22±1.3 for over 8 months. All five performed viral cultures were positive and genomic analysis confirmed a persistent infection with the same strain. Viremia resulted positive in three out of four COVID-19 clinical relapses and cleared each time after remdesivir treatment. T and NK cells dynamic was different in aviremic and viremic samples and no SARS-CoV-2 specific antibodies were detected throughout the disease course. Interpretation In our patient, SARS-CoV-2 persisted with proven infectivity for over eight months. Viremia was associated with COVID-19 relapses and remdesivir treatment was effective in viremia clearance and symptoms remission, although it was unable to clear the virus from the upper respiratory airways. During the viremic phase, we observed a low frequency of terminal effector CD8+ T lymphocytes in peripheral blood that are probably recruited in inflammatory tissue for viral eradication. In addition we found a high level of NK cells repertoire perturbation with a relevant involvement during SARS-CoV-2 viremia. Funding None."
Source: https://www.medrxiv.org/content/10.1101/2021.01.23.21249554v1
Commentary: An astonishing case study of someone who remained infectious with live virus for EIGHT MONTHS. That's a long, long haul to be contagious and presumably a spreader.
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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 or better mask if you can obtain 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. 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.