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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For my American friends: go vote if you haven't already done so. If you've voted, make sure all your friends and family do so as well.
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How much more dangerous is COVID-19? A new seroprevalence study shows an infection fatality rate of 0.97%. That's 96x more deadly than the flu.
"The first seropositive samples in our study were already detected during the week of February 23, one week before the first confirmed SARS-CoV-2 case in NYC was identified suggesting that SARS-CoV-2 was likely introduced to the NYC area several weeks earlier than previously assumed. This would not be unexpected given the unique diversity and connectivity of NYC and the large numbers of travelers that were arriving from SARS-CoV-2 affected regions of the world in January and February of 2020. The antibody titers of initial positives were low, which is consistent with slower seroconversion of perhaps mild cases.9–13 Of course, we cannot exclude with absolute certainty that some of the lower positive titers are false positives since the initially low seroprevalence falls within the confidence intervals of the PPV.
Of note, the seroprevalence in the RC group (as well as the UC group in the end of May, post peak) falls significantly below the threshold for potential community immunity, which has been estimated by one study to require at least a seropositivity rate of 67% for SARS-CoV-2.4 Based on the population of NYC (8.4 million), we estimate that by the week ending May 24, approximately 1,7 million individuals had been infected with SARS-CoV-2. Taking into account the cumulative deaths in the city by May 19 (16,674), this suggests a preliminary IFR of 0.97% (with the assumption that both seroconversion and death occur with similar delays). This is in stark contrast to the IFR of the 2009 H1N1 pandemic which was estimated to be 0.01%-0.001%.17"
Source: https://www.nature.com/articles/s41586-020-2912-6
Commentary: None of this should be news; COVID-19 is deadlier than the flu by a substantial margin. Having new data just reinforces it - keep it away from you and yours.
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How does SARS-CoV-2 work? A fascinating read:
"TenOever’s team quickly discovered that sars-CoV-2 was uncannily good at disrupting cellular programming. A typical virus replaces less than one per cent of the software in the cells it infects. With sars-CoV-2, tenOever said, about sixty per cent of the RNA in an infected cell is of viral origin—“which is the highest I’ve ever seen. Polio comes close.” Among other things, the virus rewires the alarm system that cells use to warn others about infection. Normally, as part of what is known as the “innate” immune response—so called because it is genetically hardwired, and not tailored to a specific pathogen—a cell sends out two kinds of signals. One signal, carried by molecules called interferons, travels to neighboring cells, telling them to build defenses that slow viral spread. Another signal, transmitted through molecules called cytokines, gets a message to the circulatory system’s epithelial lining. The white blood cells summoned by this second signal don’t just eat invaders and infected cells; they also gather up their dismembered protein parts. Elsewhere in the immune system, these fragments are used to create virus-specific antibodies, as part of a sophisticated “adaptive” response that can take six or seven days to develop.
Usually, the viruses that humans care about are successful because they shut down both of these signalling programs. The coronavirus is different. “It seems to block only one of those two arms,” tenOever told me. It inhibits the interferon response but does nothing about the cytokines; it evades the local defenses but allows the cells it infects to call for reinforcements. White blood cells are powerful weapons: they arrive on an inflammatory tide, destroying cells on every side, clogging up passages with the wreckage. They are meant to be used selectively, on invaders that have been contained in a small area. With the coronavirus, they are deployed too widely—a carpet bombing, rather than a surgical strike. As they do their work, inflammation distends the lungs, and debris fills them like a fog.
In late May, tenOever’s team shared its findings in the biweekly journal Cell. In their article, they argued that it’s this imbalanced immune response that gives severe covid-19—which can sometimes cause blood clots, strange swelling in children, and ultra-inflammatory “cytokine storms”—the character of an autoimmune disorder. As the virus spreads unchecked through the body, it drags a destructive immune reaction behind it. Individuals with covid-19 face the same challenge as nations during the pandemic: if they can’t contain small sites of infection early—so that a targeted response can root them out—they end up mounting interventions so large that the shock inflicts its own damage."
Source: https://www.newyorker.com/magazine/2020/11/09/how-the-coronavirus-hacks-the-immune-system
Commentary: This was a fascinating read; the fact that the virus behaves SO differently than other viruses is concerning. COVID-19 is the practice run, in case it's not clear. With an infection fatality rate only around 1%, it's the practice run for a much deadlier pandemic in the future. How your nation/region has performed in COVID-19 is how it will perform in much more dire circumstances, and for some of the most populous nations on Earth, that's not good news.
SARS-CoV-2 also could mutate again, especially as we deploy more countermeasures and eventually get good at controlling it. Mutations are nature's response to countermeasures, from increases in infectivity to lethality.
What I hope you've taken away from the last 8 months and the 12-14 months ahead is what you need to do to survive and thrive in a challenging environment.
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If we want to stop household transmission, we're going to have to relocate people. "We used contact tracing data from 7770 close contacts (1863 household contacts, 2319 work contacts, and 3588 social contacts) of PCR-confirmed COVID-19 cases who were placed under 2-week quarantine and referred for PCR testing if symptomatic. Additionally, a subset of 1150 close contacts (524 household contacts, 207 work contacts, and 419 social contacts) consented for serology testing after completion of quarantine and were assessed by a detailed symptom and risk factor questionnaire. Extensive contact tracing, thorough follow-up of contacts during and after quarantine, and low community prevalence enabled clear case–contact relationships to be established and rigorous asymptomatic case identification. Using Bayesian modelling, we estimated that the symptom-based PCR testing strategy missed more than half of SARS-CoV-2 positive close contacts and that more than a third of SARS-CoV-2-positive close contacts were asymptomatic. The risk factor analysis identified longer duration of verbal interaction and sharing a bedroom as independent exposure risk factors of SARS-CoV-2 transmission to household close contacts. For non-household close contacts, the exposure risk factors independently associated with SARS-CoV-2 transmission were longer duration of verbal interaction, sharing a vehicle, and having contact with more than one index case. Among both household and non-household contacts, indirect contact, meal-sharing, and lavatory co-usage were not independently associated with SARS-CoV-2 transmission.
The available findings, including those from our study, support physical distancing and minimising verbal interactions as part of community measures for prevention of SARS-CoV-2 transmission. In view of the substantial prevalence of asymptomatic infections, routine testing of close contacts regardless of symptoms will reduce missed diagnoses. Household close contacts, who are at high risk of SARS-CoV-2 transmission, should be prioritised for routine testing. Detection of SARS-CoV-2-positive household close contacts would prompt either relocation of the person out of the household or implementation of physical distancing and other infection prevention measures within the household."
Source: https://www.thelancet.com/journals/laninf/article/PIIS1473-3099(20)30833-1/fulltext
Commentary: Talking and sharing spaces spreads the disease. As household transmission becomes a greater problem in the fall and winter, governments need to take a serious look at providing quarantine facilities (like all those unused hotel rooms) for people in isolation so they don't continue to create household spread.
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Wastewater detection for schools?
"SARS-CoV-2 RNA fragments have been isolated from numerous wastewater treatment works, septic tanks, sewers, hospital wastewater treatment systems, and environmental discharge points7 and reported to predate the clinical diagnosis of cases,9, 10 raising the potential for its use within an early warning system. Data at a local community level have the potential to proactively inform public health-care strategies (targeting resources with associated time and cost savings) and mitigate escalating demands on health-care providers, especially during the winter months. However, monitoring occurrence or prevalence at the inlet of a wastewater treatment plant does not allow the identification of specific groups of the population, limiting its epidemiological value for managing COVID-19 and breaking chains of transmission. More recently, the wastewater-based epidemiology approach has been successfully used for near-source tracking (NST)—eg, in the sewage drains serving buildings—permitting detection of small clusters or even individual COVID-19 cases. NST, used in combination with targeted clinical testing, has clear potential to stop outbreaks and is now being used across Estonia, Finland, France, Singapore, Turkey, the UK, and the USA. NST might be more easily justified for the more vulnerable or higher risk and undersampled groups such as people in hospitals, prisons, elderly care homes, schools (particularly boarding schools), preschool settings, and factories. Although wastewater-based epidemiology cannot replace clinical testing, routine wastewater surveillance across spatial scales (from sewershed to building to sub-building level) could enable the early identification of local outbreaks through informing the targeted use of local clinical testing (ie, when and where) to capture asymptomatic and presymptomatic cases.
Experience from the past month in most of the countries in which the school year has restarted is that as community cases rise, more children become infected. Wastewater-based epidemiology using NST provides public health officials insight into the carriage of COVID-19 within discrete groups of people for whom rapid action could alleviate the risk of a much larger outbreak. Wastewater NST could be the first line of defence for high-risk populations and could offer long-term advances in public health surveillance after COVID-19.""
Source: https://www.thelancet.com/journals/lanmic/article/PIIS2666-5247(20)30193-2/fulltext
Commentary: Wastewater detection for schools is a great idea because it can aggregate the virus in a population where any one individual might not have enough viral particles to reliably test. If 30 kids have COVID-19, you'll get enough signal from wastewater to know there's a problem, even if you can't pinpoint the individual - and that can be enough to close down a facility for a temporary period of time.
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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.