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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eLifeSciences has a fantastic infographic summarizing clinical characteristics of SARS-CoV-2. "Even though this calculation is highly simplified, ignoring the effects of 'super-spreaders', herd-immunity and incomplete testing, it emphasizes the fact that viruses can spread at a bewildering pace when no countermeasures are taken. This illustrates why it is crucial to limit the spread of the virus by physical distancing measures."
Source: https://elifesciences.org/articles/57309
The whole page is an excellent read, filled with facts and data that are useful for understanding the virus in more depth. One of the juicy tidbits:
"One interesting facet of coronaviruses is that they have the largest genomes of any known RNA viruses (≈30 kb). These large genomes led researchers to suspect the presence of a 'proofreading mechanism' to reduce the mutation rate and stabilize the genome."
If anything, this means that SARS-CoV-2 may mutate LESS than influenza or the common cold - and that speaks well to vaccine efforts.
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An excellent thread via Kai Kupferschmidt.
"By now, most people are probably familiar with the reproduction number R. R=3 means that on average every infected person in turn infects three others. But the emphasis here should be on “average”!"
Source:
"In reality, some people infect a lot of people and others infect no-one. In fact - and this still blows my mind - in the datasets for every disease he looked at
@jlloydsmith told me, most people do not spread the disease."
Source:
"How uneven the distribution of spread is differs from pathogen to pathogen. Some diseases cluster more than others. And here is the important part: Coronaviruses like Sars and Mers are champions of clustering. Their spread is particulary “patchy”."
Source:
"In his 2005 Nature paper which keeps coming up in very conversation I have about this
@jlloydsmith examined eight diseases: SARS had the lowest k: 0,16. It clusters the most.
Source:
"Scientists don’t have a good handle yet on k for #SARSCoV2. But this paper by
@AdamJKucharski estimates it could be as low as 0.1, “suggesting that 80% of secondary transmissions may have been caused by a small fraction of infectious individuals (~10%)” https://wellcomeopenresearch.org/articles/5-67"
Source:
"A low dispersion factor k might explain some features of this pandemic that I have struggled to understand, for instance, why the virus did not take off everywhere sooner after it emerged in China or that report of an early case in France."
Source:
"I’ll write more about this tomorrow (late here in Berlin already), but one important point is what this means for controlling #covid19 spread. It suggests that two of the most effective parts of #PhysicalDistancing were stopping big gatherings and having people work from home."
Source:
The full writeup is here: https://www.sciencemag.org/news/2020/05/why-do-some-covid-19-patients-infect-many-others-whereas-most-don-t-spread-virus-all
The implications of this writing are clear: large gatherings of people are what cause COVID-19 to spread. Some people are super spreaders. Other people are not. We don't know why, but it also explains why test/trace/isolate is how countries like South Korea put out the fire. If only a fraction of people are super spreaders, isolating everyone who has the disease will stop it in its tracks.
What does that mean for us? It means every country in the world needs to test, test, test, test, test. Test everyone, test everywhere, test frequently. Once that's in motion, if this disease really spreads poorly at the median and only a few super spreaders are responsible for its widespread effects, then we could get a handle on this pandemic well before a vaccine is available.
That means it's up to all of us to lobby like hell for rampant testing in every jurisdiction. What if you had 5-minute testing at every major place like airports, conference centers, gyms, schools, etc.? You could stop outbreaks for one, but for another, you could potentially shut down the disease entirely.
This is technologically within our grasp today, right now. It's a question of whether our governments are willing to make the investment. Tell them to do so.
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Peer-reviewed CDC research shows another super-spreader event: choir practice. "Following a 2.5-hour choir practice attended by 61 persons, including a symptomatic index patient, 32 confirmed and 20 probable secondary COVID-19 cases occurred (attack rate = 53.3% to 86.7%); three patients were hospitalized, and two died. Transmission was likely facilitated by close proximity (within 6 feet) during practice and augmented by the act of singing. The potential for superspreader events underscores the importance of physical distancing, including avoiding gathering in large groups, to control spread of COVID-19. Enhancing community awareness can encourage symptomatic persons and contacts of ill persons to isolate or self-quarantine to prevent ongoing transmission."
Source: https://www.cdc.gov/mmwr/volumes/69/wr/mm6919e6.htm
COVID-19 is a crowd-based, indoor disease. Stay away from crowds. Stay physically distanced from others. Stay out of public indoor spaces.
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New clinical data from NYC via the Lancet including major findings of outcomes. "We prospectively characterised the epidemiology, clinical course, and outcomes of 257 critically ill patients with laboratory-confirmed COVID-19 admitted to two hospitals in New York City over the first month of the city's outbreak. Consistent with reports from Italy and China, older age and cardiopulmonary comorbidities were associated with increased mortality. Among critically ill adults with COVID-19 admitted to two hospitals in New York City during the first month of the city's outbreak, the majority were men over 60 years of age with hypertension and diabetes, nearly half had obesity, and 5% were health-care workers. 79% of patients received IMV and a third received RRT. As of April 28, 2020, 39% of patients had died in hospital. Novel findings in this study include determining independent associations between biomarkers for inflammation (interleukin-6) and thrombosis (D-dimer) and mortality, as well as identifying a high incidence of critical illness among racial and ethnic minorities in the current epicentre of the COVID-19 pandemic. Strengths of this study include prospective and complete collection of detailed clinical data and outcomes, and use of multivariable, time-varying analyses to quantify independent risk factors for in-hospital death in one of the largest studies to date of critically ill patients with COVID-19 in the USA."
Source: https://www.thelancet.com/journals/lancet/article/PIIS0140-6736(20)31189-2/fulltext
Until now, we've been relying on data from other countries to determine courses of action for COVID-19 in America. With these new datasets, we're starting to see the impact in America, with the American population which tends to be: sicker, higher-risk, more obese.
If you get critically ill with COVID-19 in America, you have a roughly 39% chance of dying.
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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.
2. Wear gloves and a mask when out of your home. Consider wearing a face shield.
3. Stay home as much as possible.
4. Get your personal finances in order now. Cut all unnecessary costs.
5. Donate any PPE you can. https://getusppe.org/give/
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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/
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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.