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.
--
An important clarification on basic math. Yes, the death rate of COVID-19 is going down. Why? The disease isn't any less deadly. It's because there are many, many more cases. It's simple math: if the numerator of a fraction is the same, but the denominator increases, the rate goes down.
1 death per 100 cases = 1% death rate in this moment in time
Now, suppose you suddenly, like overnight, get 900 new cases.
1 death per 1,000 cases = 0.1% death rate in this moment in time
Has the disease changed? No. You just have many, many more cases rapidly. And because deaths typically take 4-6 weeks, in any environment where cases are increasing rapidly, the death rate will always seem lower for a while... until it's not. The reverse will be true as well - after a region locks down, cases decline while death rates remain high, making the disease seem worse than it is.
--
A study of COVID-19 in homelessness. "Dr. Gaeta: In the United States, more than half a million people are homeless on any given night.12 Those staying in congregate shelters — where SARS-CoV-2 may spread rapidly and among asymptomatic people — are at a particularly high risk for the development of Covid-19. The risk is even higher among the large proportion of homeless people who have underlying heart, lung, or metabolic disorders or are in an older age group. Universal testing for SARS-CoV-2 infection at shelters is valuable when community transmission is mounting or a shelter-based cluster of Covid-19 cases has been identified, and when resources permit. Symptom screening alone will miss a large number of cases in such instances. It is critical for patients to have private space to isolate and recover from Covid-19 in order to mitigate the spread of the virus, but private housing is a privilege that is not afforded to all. Collaborative efforts among health care entities, homeless service providers, and government must ensure that a Covid-19 response system for the homeless population includes the development of adequate isolation and quarantine sites. The toll that Covid-19 has taken — and will continue to take — on homeless people in Boston lays bare the health risks associated with having no home and is a stark reminder of the need to address widespread homelessness in our country."
Source: https://www.nejm.org/doi/full/10.1056/NEJMcpc2002421
Commentary: Shelters and prisons are ideal breeding grounds for COVID-19. To permanently stifle the pandemic, we have to flush it out of every possible reservoir where it lurks - and that means dealing with homelessness in a medically effective, humane way.
--
Neither pigs nor chickens can be infected with COVID19. "We found that neither pigs nor chickens showed any signs of infection and none of the contact animals became infected. This finding is of particular importance for risk analysis in these farmed animals, which are kept in large numbers and in contact with humans. Moreover, the virus replicated in the upper respiratory tract of fruit bats, and was transmitted to contact animals. This finding indicates that fruit bats, which are kept and bred in captivity, can serve as a reservoir host model, but also emphasises the risk to free-living bats (eg, in ecological bat protection programmes). Finally, ferret infections resulted in a high replication rate of SARS-CoV-2 in the nasal cavity, as confirmed by immunohistochemistry and in situ hybridisation. The transmission to contacts was highly efficient and high virus titres were detected in the ferrets' nasal cavities. We showed that only minor viral adaptions occurred during infection of ferrets with a human SARS-CoV-2 isolate. Our results suggest that the ferret is a highly suitable model for testing vaccines and antiviral treatment for their effect on viral excretion and transmission."
Source: https://www.thelancet.com/journals/lanmic/article/PIIS2666-5247(20)30089-6/fulltext
Commentary: In addition to identifying COVID-19 safety for humans working with pigs and chickens in a food production environment (the danger is other humans, not the animals), the study suggests ferrets as test animals, which is good for helping accelerate the vaccine process.
--
SARS-CoV-2 may not have come from bats directly, but by an intermediary, according to genomic analysis. "Together, our structural and biochemical data indicate that a bat virus, similar to RaTG13, would not be able to bind effectively to human ACE2 receptor and would be unlikely to infect humans directly. Given the modular nature of the human and bat S glycoproteins, and the number and structural locations of the amino-acid-sequence differences between them, our observations support the involvement of recombination8 between distinct coronavirus genomes in the generation of SARS-CoV-2. The structure of the SARS-CoV-2 S protein presented here is at high resolution and is nearly complete, and has many more external loops included than previously reported structures do, providing important insights for vaccine design. Furthermore, our study suggests that the presence of the furin-cleavage site in the S protein of SARS-CoV-2 facilitates the conformational change required for RBD exposure and binding to surface receptors."
Source: https://www.nature.com/articles/s41594-020-0468-7.pdf
Commentary: The quest continues for where SARS-CoV-2 came from, but this newest genomic analysis suggests it wasn't directly from a bat, but some other animal intermediary.
--
No Animal House? "UC Berkeley has seen 47 new COVID-19 cases, which resulted primarily from “a series of recent parties connected to the CalGreek system” over the course of a single week, the university reported Wednesday.
Cal described the “notable increase” as “concerning,” particularly because UC Berkeley had previously tallied only 23 coronavirus infections since the outbreak began. That’s a 104% increase.
“The majority of these new cases stem from a series of recent parties connected to the CalGreek system, which included students both within the CalGreek community and others, and led to some secondary spread within households and within other smaller gatherings,” according to the statement from UC Berkeley University Health Services Medical Director Anna Harte and Assistant Vice Chancellor Guy Nicolette. “Generally, these infections are directly related to social events where students have not followed basic safety measures such as physical distancing, wearing face coverings, limiting event size, and gathering outside.”"
Source: https://www.berkeleyside.com/2020/07/08/uc-berkeley-has-47-new-covid-19-cases-mostly-from-week-of-frat-parties
Commentary: Absolutely no surprise that a frat party - which is functionally just another bar/nightclub environment - would spread COVID-19. Stay out of public gatherings indoors.
--
Indoor disease. "A surge in coronavirus cases in and around Tulsa, Okla., is probably connected to the campaign rally President Trump held there last month, the city’s top health official said on Wednesday.
Tulsa County reported 206 new confirmed cases on Tuesday and 261 — a record high — on Monday, and Dr. Bruce Dart, the director of the Tulsa Health Department, said at a news conference that it was reasonable to link the spike to the rally and related events.
“The past two days we’ve had almost 500 cases, and we know we had several large events a little over two weeks ago, which is about right,” Dr. Dart said. “So I guess we just connect the dots.”
Asked whether contact tracing had confirmed a link between the rally and the increase in cases, Leanne Stephens, a spokeswoman for the health department, said it “will not publicly identify any individual or facility at risk of exposure, or where transmission occurred.”
Ms. Stephens said this week that contact tracers had been “completely inundated” trying to track down dozens of close contacts for thousands of confirmed cases, a task that can take hours for each person.
Karen Keith, a county commissioner in Tulsa who oversees the area where the rally occurred, said in an interview on Wednesday that contact tracers were struggling to persuade people to reveal where they had been, frustrating local officials.
She added that a surge in cases in rural parts of the state was most likely another indication that the rally could be responsible for the most recent outbreaks. Dr. Dart told The Tulsa World newspaper that he had examined Google mobility data for rally attendees, which offered a “ballpark” idea of where they had settled after the event."
Source: https://www.nytimes.com/2020/07/08/us/politics/coronavirus-tulsa-trump-rally.html
Commentary: Stay out of indoor locations. Stay away from others. Wear a mask. Watch your distance. Wash your hands.
--
Don't rule out interstate travel restrictions. "“It's certainly the case that travel from places with a lot of COVID-19 is a major source of infection in places that have cleared it. And what we will see inevitably and are seeing already around the world and potentially around the U.S. are restrictions on travel from places that don't have it under control by places that do have it under control. It's almost unthinkable that something like that would happen in the United States, but on the other hand, if the differences are so enormous, it's almost unthinkable that that wouldn't happen here.
“On the one hand, we do want economic activity returning, and if people are traveling among areas with similar levels of spread, that reduces the likelihood that you'll increase the spread. But anytime there's travel from a place with a lot of COVID-19 to a place with not much COVID-19, you have a high risk of it spreading.”"
Source: https://www.wbur.org/hereandnow/2020/07/06/covid-19-cdc-tom-frieden
Commentary: Travel between states is something that's Constitutionally mandated, but there's nothing saying that the government can't impose restrictions for public health purposes once you arrive in a different state - like a mandatory quarantine. If the pandemic continues to worsen, that may become necessary, and while it will likely be challenged in court, by the time the court case is over, so will the pandemic, hopefully.
--
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. Wear gloves and a mask when out of your home. Consider wearing a face shield if you can't breathe at all through a mask. 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. Avoid indoor places as much as you can.
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.
--
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
--
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.